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Gonuguntla HN, Surendra KSNL, Prasad A, Sarangi LN, Rana SK, Manasa G, Muthappa PN, Harikumar AV, Sharma GK. Brucella melitensis: Divergence Among Indian Strains and Genetic Characterization of a Strain Isolated from Cattle. Indian J Microbiol 2023; 63:272-280. [PMID: 37781017 PMCID: PMC10533427 DOI: 10.1007/s12088-023-01081-w] [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: 11/30/2022] [Accepted: 06/17/2023] [Indexed: 10/03/2023] Open
Abstract
Brucella melitensis primarily affects sheep, goats and is associated with brucellosis in humans, which is one of the world's most widespread neglected zoonotic disease. The current study attempted the determination of genetic diversity through comparative genome analysis of B. melitensis strains reported from India with other countries. The study also reports the isolation and identification of B. melitensis BMNDDB8664 from a cow with a history of abortion, whole-genome sequencing (WGS), determination of virulence factors, genotyping, and comparative genome analysis. Multilocus sequence typing, Multiple locus variable number of tandem repeats analysis (MLVA), and WGS based phylogeny revealed the predominance of ST-8 and genotypes (116 and II respectively) that clustered to the East Mediterranean lineage. Identification of hitherto unreported genotypes by MLVA also indicated the existence and circulation of West Mediterranean and American lineages in India. Though the AMOS-PCR results suggest the BMNDDB8664 isolate as Brucella abortus, the outcomes from multiplex PCR, ribosomal multilocus sequence typing, and WGS analysis confirmed it as B. melitensis. The analysis revealed the presence of adeF gene (aids conferring resistance to fluoro-quinolone and tetracyclines). The isolate lacked two important T4SS genes virB2 and virB7 genes (roles in infection and rifampicin resistance respectively) and also lacked the Brucella suis mprF gene that aids intracellular survival. Further, BMNDDB8664 lacked some of the genes associated with LPS synthesis (wbkB, wbkC) and transport (wzm, wzt) and hence, is most likely a rough strain. WGS-based phylogenetic analysis revealed close genetic relatedness of this BMNDDB8664 with a sheep isolate and two human isolates. The results prompt systematic, broad-based epidemiological studies on brucella infection at the species level. For effective control of human brucellosis, a concerted One Health approach with studies encircling the identification of aetiology at species, strain level to find their prevalence, spread, and inter-host transmission patterns need to be understood, for better design and implementation of effective control strategies in India and other endemic regions. Supplementary Information The online version contains supplementary material available at 10.1007/s12088-023-01081-w.
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Affiliation(s)
- Hariprasad Naidu Gonuguntla
- National Dairy Development Board Research and Development Laboratory, IIL Campus, Gachibowli, Hyderabad, Telangana 500032 India
| | - Kota Sri Naga Leela Surendra
- National Dairy Development Board Research and Development Laboratory, IIL Campus, Gachibowli, Hyderabad, Telangana 500032 India
| | - Amitesh Prasad
- National Dairy Development Board Research and Development Laboratory, IIL Campus, Gachibowli, Hyderabad, Telangana 500032 India
| | - Laxmi Narayan Sarangi
- National Dairy Development Board Research and Development Laboratory, IIL Campus, Gachibowli, Hyderabad, Telangana 500032 India
| | | | - Gujjala Manasa
- National Dairy Development Board Research and Development Laboratory, IIL Campus, Gachibowli, Hyderabad, Telangana 500032 India
| | - Ponnanna Nadikerianda Muthappa
- National Dairy Development Board Research and Development Laboratory, IIL Campus, Gachibowli, Hyderabad, Telangana 500032 India
| | - A. V. Harikumar
- National Dairy Development Board, Anand, Gujarat 388001 India
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Kurmanov B, Zincke D, Su W, Hadfield TL, Aikimbayev A, Karibayev T, Berdikulov M, Orynbayev M, Nikolich MP, Blackburn JK. Assays for Identification and Differentiation of Brucella Species: A Review. Microorganisms 2022; 10:microorganisms10081584. [PMID: 36014002 PMCID: PMC9416531 DOI: 10.3390/microorganisms10081584] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/26/2022] [Accepted: 07/28/2022] [Indexed: 11/16/2022] Open
Abstract
Brucellosis is one of the most important and widespread bacterial zoonoses worldwide. Cases are reported annually across the range of known infectious species of the genus Brucella. Globally, Brucella melitensis, primarily hosted by domestic sheep and goats, affects large proportions of livestock herds, and frequently spills over into humans. While some species, such as Brucella abortus, are well controlled in livestock in areas of North America, the Greater Yellowstone Ecosystem supports the species in native wild ungulates with occasional spillover to livestock. Elsewhere in North America, other Brucella species still infect domestic dogs and feral swine, with some associated human cases. Brucella spp. patterns vary across space globally with B. abortus and B. melitensis the most important for livestock control. A myriad of other species within the genus infect a wide range of marine mammals, wildlife, rodents, and even frogs. Infection in humans from these others varies with geography and bacterial species. Control in humans is primarily achieved through livestock vaccination and culling and requires accurate and rapid species confirmation; vaccination is Brucella spp.-specific and typically targets single livestock species for distribution. Traditional bacteriology methods are slow (some media can take up to 21 days for bacterial growth) and often lack the specificity of molecular techniques. Here, we summarize the molecular techniques for confirming and identifying specific Brucella species and provide recommendations for selecting the appropriate methods based on need, sensitivity, and laboratory capabilities/technology. As vaccination/culling approaches are costly and logistically challenging, proper diagnostics and species identification are critical tools for targeting surveillance and control.
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Affiliation(s)
- Berzhan Kurmanov
- Spatial Epidemiology & Ecology Research Lab, Department of Geography, University of Florida, Gainesville, FL 32611, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA
| | - Diansy Zincke
- Spatial Epidemiology & Ecology Research Lab, Department of Geography, University of Florida, Gainesville, FL 32611, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA
| | - Wanwen Su
- Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Ted L. Hadfield
- Spatial Epidemiology & Ecology Research Lab, Department of Geography, University of Florida, Gainesville, FL 32611, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA
| | - Alim Aikimbayev
- Scientific Practical Center for Sanitary Epidemiological Expertise and Monitoring, Ministry of Health, Almaty 050008, Kazakhstan
| | - Talgat Karibayev
- National Reference Veterinary Center, Nur-Sultan 010000, Kazakhstan
| | - Maxat Berdikulov
- National Reference Veterinary Center, Nur-Sultan 010000, Kazakhstan
| | - Mukhit Orynbayev
- Research Institute for Biological Special Problems, Otar, Zhambyl 080409, Kazakhstan
| | - Mikeljon P. Nikolich
- Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Jason K. Blackburn
- Spatial Epidemiology & Ecology Research Lab, Department of Geography, University of Florida, Gainesville, FL 32611, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA
- Correspondence:
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High-Resolution Melting PCR as Rapid Genotyping Tool for Brucella Species. Microorganisms 2022; 10:microorganisms10020336. [PMID: 35208791 PMCID: PMC8876322 DOI: 10.3390/microorganisms10020336] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/26/2022] [Accepted: 01/28/2022] [Indexed: 02/06/2023] Open
Abstract
Brucella sp. are the causative agents of brucellosis. One of the main characteristics of the Brucella genus concerns its very high genetic homogeneity. To date, classical bacteriology typing is still considered as the gold standard assay for direct diagnosis of Brucella. Molecular approaches are routinely used for the identification of Brucella at the genus level. However, genotyping is more complex, and to date, no method exists to quickly assign a strain into species and biovar levels, and new approaches are required. Next generation sequencing (NGS) opened a new era into the diagnosis of bacterial diseases. In this study, we designed a high-resolution melting (HRM) method for the rapid screening of DNA and direct assignment into one of the 12 species of the Brucella genus. This method is based on 17 relevant single nucleotide polymorphisms (SNPs), identified and selected from a whole genome SNP (wgSNP) analysis based on 988 genomes (complete and drafts). These markers were tested against the collection of the European Reference Laboratory (EU-RL) for brucellosis (1440 DNAs extracted from Brucella strains). The results confirmed the reliability of the panel of 17 SNP markers, allowing the differentiation of each species of Brucella together with biovars 1, 2, and 3 of B. suis and vaccine strain Rev1 (B. melitensis) within 3 h, which is a considerable gain of time for brucellosis diagnosis. Therefore, this genotyping tool provides a new and quick alternative for Brucella identification based on SNPs with the HRM-PCR assay.
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Whatmore AM, Foster JT. Emerging diversity and ongoing expansion of the genus Brucella. INFECTION GENETICS AND EVOLUTION 2021; 92:104865. [PMID: 33872784 DOI: 10.1016/j.meegid.2021.104865] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 12/15/2022]
Abstract
Remarkable genetic diversity and breadth of host species has been uncovered in the Brucella genus over the past decade, fundamentally changing our concept of what it means to be a Brucella. From ocean fishes and marine mammals, to pond dwelling amphibians, forest foxes, desert rodents, and cave-dwelling bats, Brucella have revealed a variety of previously unknown niches. Classical microbiological techniques have been able to help us classify many of these new strains but at times have limited our ability to see the true relationships among or within species. The closest relatives of Brucella are soil bacteria and the adaptations of Brucella spp. to live intracellularly suggest that the genus has evolved to live in vertebrate hosts. Several recently discovered species appear to have phenotypes that are intermediate between soil bacteria and core Brucella, suggesting that they may represent ancestral traits that were subsequently lost in the traditional species. Remarkably, the broad relationships among Brucella species using a variety of sequence and fragment-based approaches have been upheld when using comparative genomics with whole genomes. Nonetheless, genomes are required for fine-scale resolution of many of the relationships and for understanding the evolutionary history of the genus. We expect that the coming decades will reveal many more hosts and previously unknown diversity in a wide range of environments.
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Affiliation(s)
- Adrian M Whatmore
- OIE and FAO Brucellosis Reference Laboratory, Department of Bacteriology, Animal and Plant Health Agency (APHA), Woodham Lane, Addlestone, Surrey, United Kingdom.
| | - Jeffrey T Foster
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
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Whole Genome Sequence Analysis of Brucella abortus Isolates from Various Regions of South Africa. Microorganisms 2021; 9:microorganisms9030570. [PMID: 33799545 PMCID: PMC7998772 DOI: 10.3390/microorganisms9030570] [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: 11/30/2020] [Revised: 02/10/2021] [Accepted: 02/15/2021] [Indexed: 11/17/2022] Open
Abstract
The availability of whole genome sequences in public databases permits genome-wide comparative studies of various bacterial species. Whole genome sequence-single nucleotide polymorphisms (WGS-SNP) analysis has been used in recent studies and allows the discrimination of various Brucella species and strains. In the present study, 13 Brucella spp. strains from cattle of various locations in provinces of South Africa were typed and discriminated. WGS-SNP analysis indicated a maximum pairwise distance ranging from 4 to 77 single nucleotide polymorphisms (SNPs) between the South African Brucella abortus virulent field strains. Moreover, it was shown that the South African B. abortus strains grouped closely to B. abortus strains from Mozambique and Zimbabwe, as well as other Eurasian countries, such as Portugal and India. WGS-SNP analysis of South African B. abortus strains demonstrated that the same genotype circulated in one farm (Farm 1), whereas another farm (Farm 2) in the same province had two different genotypes. This indicated that brucellosis in South Africa spreads within the herd on some farms, whereas the introduction of infected animals is the mode of transmission on other farms. Three B. abortus vaccine S19 strains isolated from tissue and aborted material were identical, even though they originated from different herds and regions of South Africa. This might be due to the incorrect vaccination of animals older than the recommended age of 4-8 months or might be a problem associated with vaccine production.
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Kılıç S, Çelebi B, Turan M. Brucella melitensis and Brucella abortus genotyping via real-time PCR targeting 21 variable genome loci. J Microbiol Methods 2020; 180:106125. [PMID: 33333100 DOI: 10.1016/j.mimet.2020.106125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 12/11/2020] [Accepted: 12/11/2020] [Indexed: 11/18/2022]
Abstract
Brucella melitensis and Brucella abortus account for almost all cases of brucellosis in Turkish population. We developed a fourplex quantitative real-time PCR (qPCR) assay for the electrophoresis-free, rapid and cost-effective differentiation of B. abortus and B. melitensis from the other Brucella spp. The 4-plex species differentiation assay was combined with a qPCR assay targeting 17 different single nucleotide polymorphism (SNP) loci in Brucella genomes. This combination resulted in a 21 Variable Genome Loci (21-VGL) qPCR assay for high resolution genotyping of B. abortus and B. melitensis. A total of 486 Brucella was analyzed using the qPCR assay to create a 21-VGL profile database. The database contained the profiles of 55 B. abortus, 352 B. melitensis, 3 B. ceti, 6 B. neotomae, 7 B. ovis, 6 B. pinnipedialis, 44 B. suis and 13 B. canis strains. The 21-VGL Brucella genotyping clearly distinguished B. abortus, B. melitensis, B. neotomae and B. ovis. The 21-VGL approach could not distinguish B. pinnipedialis from B. ceti and some B. suis genotypes from B. canis. The results revealed that more than 99% of the Brucella isolates in Turkey were B. melitensis and 21-VGL genotyping can be reduced to 8-VGL B. melitensis genotyping without any loss of genotyping resolution. To our knowledge, we introduced the fastest and the lowest-cost B. abortus and B. melitensis genotyping and species differentiation methodology in the literature.
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Affiliation(s)
- Selçuk Kılıç
- Microbiology Reference Laboratories, General Directorate of Public Health, Minister of Health, Ankara, Turkey; University of Health Sciences, Institute of Defence Health Sciences, Department of Medical CBRN, Ankara, Turkey.
| | - Bekir Çelebi
- Department of Zonotic and Vector Borne Diseases, General Directorate of Public Health, Minister of Health, Ankara, Turkey
| | - Meral Turan
- Microbiology Reference Laboratories, General Directorate of Public Health, Minister of Health, Ankara, Turkey
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Suárez-Esquivel M, Chaves-Olarte E, Moreno E, Guzmán-Verri C. Brucella Genomics: Macro and Micro Evolution. Int J Mol Sci 2020; 21:E7749. [PMID: 33092044 PMCID: PMC7589603 DOI: 10.3390/ijms21207749] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/08/2020] [Accepted: 10/11/2020] [Indexed: 01/25/2023] Open
Abstract
Brucella organisms are responsible for one of the most widespread bacterial zoonoses, named brucellosis. The disease affects several species of animals, including humans. One of the most intriguing aspects of the brucellae is that the various species show a ~97% similarity at the genome level. Still, the distinct Brucella species display different host preferences, zoonotic risk, and virulence. After 133 years of research, there are many aspects of the Brucella biology that remain poorly understood, such as host adaptation and virulence mechanisms. A strategy to understand these characteristics focuses on the relationship between the genomic diversity and host preference of the various Brucella species. Pseudogenization, genome reduction, single nucleotide polymorphism variation, number of tandem repeats, and mobile genetic elements are unveiled markers for host adaptation and virulence. Understanding the mechanisms of genome variability in the Brucella genus is relevant to comprehend the emergence of pathogens.
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Affiliation(s)
- Marcela Suárez-Esquivel
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia 3000, Costa Rica; (M.S.-E.); (E.M.)
| | - Esteban Chaves-Olarte
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José 1180, Costa Rica;
| | - Edgardo Moreno
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia 3000, Costa Rica; (M.S.-E.); (E.M.)
| | - Caterina Guzmán-Verri
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia 3000, Costa Rica; (M.S.-E.); (E.M.)
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José 1180, Costa Rica;
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Abstract
The clinical presentation of brucellosis in humans is variable and unspecific, and thus, laboratory corroboration of the diagnosis is essential for the patient's proper treatment. The diagnosis of brucellar infections can be made by culture, serological tests, and nucleic acid amplification assays. Modern automated blood culture systems enable detection of acute cases of brucellosis within the routine 5- to 7-day incubation protocol employed in clinical microbiology laboratories, although a longer incubation and performance of blind subcultures may be needed for protracted cases. Serological tests, though they lack specificity and provide results that may be difficult to interpret in individuals repeatedly exposed to Brucella organisms, nevertheless remain a diagnostic cornerstone in resource-poor countries. Nucleic acid amplification assays combine exquisite sensitivity, specificity, and safety and enable rapid diagnosis of the disease. However, long-term persistence of positive molecular test results in patients that have apparently fully recovered is common and has unclear clinical significance and therapeutic implications. Therefore, as long as there are no sufficiently validated commercial tests or studies that demonstrate an adequate interlaboratory reproducibility of the different homemade PCR assays, cultures and serological methods will remain the primary tools for the diagnosis and posttherapeutic follow-up of human brucellosis.
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Affiliation(s)
- Pablo Yagupsky
- Clinical Microbiology Laboratory, Soroka University Medical Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Pilar Morata
- Biochemistry and Molecular Biology Department, Faculty of Medicine, University of Málaga, Málaga, Spain
- IBIMA, Málaga, Spain
| | - Juan D Colmenero
- Infectious Diseases Service, University Regional Hospital, Málaga, Spain
- IBIMA, Málaga, Spain
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Ledwaba MB, Gomo C, Lekota KE, Le Flèche P, Hassim A, Vergnaud G, van Heerden H. Molecular characterization of Brucella species from Zimbabwe. PLoS Negl Trop Dis 2019; 13:e0007311. [PMID: 31107864 PMCID: PMC6544324 DOI: 10.1371/journal.pntd.0007311] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 05/31/2019] [Accepted: 03/18/2019] [Indexed: 12/30/2022] Open
Abstract
Brucella abortus and B. melitensis have been reported in several studies in animals in Zimbabwe but the extent of the disease remains poorly known. Thus, characterizing the circulating strains is a critical first step in understanding brucellosis in the country. In this study we used an array of molecular assays including AMOS-PCR, Bruce-ladder, multiple locus variable number tandem repeats analysis (MLVA) and single nucleotide polymorphisms from whole genome sequencing (WGS-SNP) to characterize Brucella isolates to the species, biovar, and individual strain level. Sixteen Brucella strains isolated in Zimbabwe at the Central Veterinary laboratory from various hosts were characterized using all or some of these assays. The strains were identified as B. ovis, B. abortus, B. canis and B. suis, with B. canis being the first report of this species in Zimbabwe. Zimbabwean strains identified as B. suis and B. abortus were further characterized with whole genome sequencing and were closely related to reference strains 1330 and 86/8/59, respectively. We demonstrate the range of different tests that can be performed from simple assays that can be run in laboratories lacking sophisticated instrumentation to whole genome analyses that currently require substantial expertise and infrastructure often not available in the developing world.
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Affiliation(s)
- Maphuti Betty Ledwaba
- Department of Veterinary Tropical Diseases, University of Pretoria, Pretoria, South Africa
| | - Calvin Gomo
- Central Veterinary Laboratory (CVL), Harare, Zimbabwe
- Chinhoyi University of Technology, Department of Animal Production and Technology, Harare, Zimbabwe
| | - Kgaugelo Edward Lekota
- Department of Veterinary Tropical Diseases, University of Pretoria, Pretoria, South Africa
| | - Philippe Le Flèche
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Ayesha Hassim
- Department of Veterinary Tropical Diseases, University of Pretoria, Pretoria, South Africa
| | - Gilles Vergnaud
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Henriette van Heerden
- Department of Veterinary Tropical Diseases, University of Pretoria, Pretoria, South Africa
- * E-mail:
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Ferreira Vicente A, Girault G, Corde Y, Souza Ribeiro Mioni M, Borges Keid L, Jay M, Megid J, Mick V. New insights into phylogeography of worldwide Brucella canis isolates by comparative genomics-based approaches: focus on Brazil. BMC Genomics 2018; 19:636. [PMID: 30153798 PMCID: PMC6114238 DOI: 10.1186/s12864-018-5001-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 08/08/2018] [Indexed: 11/20/2022] Open
Abstract
Background Canine brucellosis, due to Brucella canis, is a worldwide zoonosis that remains endemic in South America, including Brazil. Implementation of powerful whole-genome sequencing approaches allowed exploring the Brucella genus considered as monomorphic, with, to date, more than 500 genomes available in public databases. Nevertheless, with under-representation of B. canis genomes −only twenty complete or draft genomes−, lack of knowledge about this species is still considerable. This report describes a comparative genomics-based phylogeographic investigation of 53 B. canis strains, including 28 isolates paired-end sequenced in this work. Results Obtained results allow identifying a SNP panel species-specific to B. canis of 1086 nucleotides. In addition, high-resolution analyses assess the epidemiological relationship between worldwide isolates. Our findings show worldwide strains are distributed among 2 distinct lineages. One of them seems to be specific to South American strains, including Brazil. B. canis South American strains may be identified by a SNP panel of 15 nucleotides, whereas a 22 SNP panel is sufficient to define contamination origin from Brazil. These results lead to the proposal of a possible spread route for dog brucellosis through South America. Additionally, whole-genome analyses highlight the remarkable genomic stability of B. canis strains over time and the sustainability of the infection in São Paulo over 12 year-period. Conclusions Significant increase of B. canis genomes available in public databases provides new insights into B. canis infection in South America, including Brazil, as well as in the world, and also offers new perspectives for the Brucella genus largo sensu. Electronic supplementary material The online version of this article (10.1186/s12864-018-5001-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Acácia Ferreira Vicente
- EU/OIE/FAO & National Reference Laboratory for animal Brucellosis, Animal Health Laboratory, Paris-Est University/Anses, Maisons-Alfort, France.,Molecular Biology Laboratory, Dept. Veterinary Hygiene and Public Health, FMVZ, UNESP, Botucatu, Brazil
| | - Guillaume Girault
- EU/OIE/FAO & National Reference Laboratory for animal Brucellosis, Animal Health Laboratory, Paris-Est University/Anses, Maisons-Alfort, France.
| | - Yannick Corde
- EU/OIE/FAO & National Reference Laboratory for animal Brucellosis, Animal Health Laboratory, Paris-Est University/Anses, Maisons-Alfort, France.,Present Address: Physiology of reproduction and behaviour joint research unit, INRA Val de Loire Centre, Nouzilly, France
| | | | - Lara Borges Keid
- Dept. Veterinary Medicine, University of Animal Science and Food Engineering, USP, Pirassununga, Brazil
| | - Maryne Jay
- EU/OIE/FAO & National Reference Laboratory for animal Brucellosis, Animal Health Laboratory, Paris-Est University/Anses, Maisons-Alfort, France.,Present Address: Anses, Laboratoire de Lyon, UMR Mycoplasmoses des Ruminants, Lyon, France Université de Lyon, VetAgro Sup, UMR Mycoplasmoses des Ruminants, Marcy L'Etoile, France
| | - Jane Megid
- Molecular Biology Laboratory, Dept. Veterinary Hygiene and Public Health, FMVZ, UNESP, Botucatu, Brazil
| | - Virginie Mick
- EU/OIE/FAO & National Reference Laboratory for animal Brucellosis, Animal Health Laboratory, Paris-Est University/Anses, Maisons-Alfort, France.
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Tian GZ, Cui BY, Piao DR, Zhao HY, Li LY, Liu X, Xiao P, Zhao ZZ, Xu LQ, Jiang H, Li ZJ. Multi-locus variable-number tandem repeat analysis of Chinese Brucella strains isolated from 1953 to 2013. Infect Dis Poverty 2017; 6:89. [PMID: 28460642 PMCID: PMC5412030 DOI: 10.1186/s40249-017-0296-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 03/29/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Brucellosis was a common human and livestock disease caused by Brucella strains, the category B priority pathogens by the US Center for Disease Control (CDC). Identified as a priority disease in human and livestock populations, the increasing incidence in recent years in China needs urgent control measures for this disease but the molecular background important for monitoring the epidemiology of Brucella strains at the national level is still lacking. METHODS A total of 600 Brucella isolates collected during 60 years (from 1953 to 2013) in China were genotyped by multiple locus variable-number tandem repeat analysis (MLVA) and the variation degree of MLVA11 loci was calculated by the Hunter Gaston Diversity Index (HGDI) values. The charts and map were processed by Excel 2013, and cluster analysis and epidemiological distribution was performed using BioNumerics (version 5.1). RESULTS The 600 representative Brucella isolates fell into 104 genotypes with 58 singleton genotypes by the MLVA11 assay, including B. melitensis biovars 2 and 3 (five main genotypes), B. abortus biovars 1 and 3 (two main genotypes), B. suis biovars 1 and 3 (three main genotypes), and B. canis (two main genotypes) respectively. While most B. suis biovar 1 and biovar 3 were respectively found in northern provinces and southern provinces, B. melitensis and B. abortus strains were dominant in China. Canine Brucellosis was only found in animals without any human cases reported. Eight Brucellosis epidemic peaks emerged during the 60 years between 1953 and 2013: 1955 - 1959, 1962 - 1969, 1971 - 1975, 1977 - 1983, 1985 - 1989, 1992 - 1997, 2000 - 2008 and 2010 - 2013 in China. CONCLUSIONS Brucellosis has its unique molecular epidemiological patterns with specific spatial and temporal distribution according to MLVA. TRIAL REGISTRATION IDOP-D-16-00101.
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Affiliation(s)
- Guo-Zhong Tian
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Prevention and Control, Beijing, 102206, China
| | - Bu-Yun Cui
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Prevention and Control, Beijing, 102206, China
| | - Dong-Ri Piao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Prevention and Control, Beijing, 102206, China
| | - Hong-Yan Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Prevention and Control, Beijing, 102206, China
| | - Lan-Yu Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Prevention and Control, Beijing, 102206, China
| | - Xi Liu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Prevention and Control, Beijing, 102206, China
| | - Pei Xiao
- National Institute of Occupational Health and Poison Control, Chinese Center for Disease Prevention and Control, Beijing, 100050, China
| | - Zhong-Zhi Zhao
- Department of Brucellosis Prevention and Control, Qinghai Institute for Endemic Disease Prevention and Control, Xining, 811602, China
| | - Li-Qing Xu
- Department of Brucellosis Prevention and Control, Qinghai Institute for Endemic Disease Prevention and Control, Xining, 811602, China
| | - Hai Jiang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Prevention and Control, Beijing, 102206, China.
| | - Zhen-Jun Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Prevention and Control, Beijing, 102206, China.
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12
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Georgi E, Walter MC, Pfalzgraf MT, Northoff BH, Holdt LM, Scholz HC, Zoeller L, Zange S, Antwerpen MH. Whole genome sequencing of Brucella melitensis isolated from 57 patients in Germany reveals high diversity in strains from Middle East. PLoS One 2017; 12:e0175425. [PMID: 28388689 PMCID: PMC5384748 DOI: 10.1371/journal.pone.0175425] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 03/24/2017] [Indexed: 01/31/2023] Open
Abstract
Brucellosis, a worldwide common bacterial zoonotic disease, has become quite rare in Northern and Western Europe. However, since 2014 a significant increase of imported infections caused by Brucella (B.) melitensis has been noticed in Germany. Patients predominantly originated from Middle East including Turkey and Syria. These circumstances afforded an opportunity to gain insights into the population structure of Brucella strains. Brucella-isolates from 57 patients were recovered between January 2014 and June 2016 with culture confirmed brucellosis by the National Consultant Laboratory for Brucella. Their whole genome sequences were generated using the Illumina MiSeq platform. A whole genome-based SNP typing assay was developed in order to resolve geographically attributed genetic clusters. Results were compared to MLVA typing results, the current gold-standard of Brucella typing. In addition, sequences were examined for possible genetic variation within target regions of molecular diagnostic assays. Phylogenetic analyses revealed spatial clustering and distinguished strains from different patients in either case, whereas multiple isolates from a single patient or technical replicates showed identical SNP and MLVA profiles. By including WGS data from the NCBI database, five major genotypes were identified. Notably, strains originating from Turkey showed a high diversity and grouped into seven subclusters of genotype II. MLVA analysis congruently clustered all isolates and predominantly matched the East Mediterranean genetic clade. This study confirms whole-genome based SNP-analysis as a powerful tool for accurate typing of B. melitensis. Furthermore it allows special allocation and therefore provides useful information on the geographic origin for trace-back analysis. However, the lack of reliable metadata in public databases often prevents a resolution below geographic regions or country levels and corresponding precise trace-back analysis. Once this obstacle is resolved, WGS-derived bacterial typing adds an important method to complement epidemiological surveys during outbreak investigations. This is the first report of a detailed genetic investigation of an extensive collection of B. melitensis strains isolated from human cases in Germany.
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Affiliation(s)
- Enrico Georgi
- Bundeswehr Institute of Microbiology, Munich, Germany
| | | | | | - Bernd H. Northoff
- Institute of Laboratory Medicine, Ludwig-Maximilians University, Munich, Germany
| | - Lesca M. Holdt
- Institute of Laboratory Medicine, Ludwig-Maximilians University, Munich, Germany
| | - Holger C. Scholz
- Bundeswehr Institute of Microbiology, Munich, Germany
- National Consultant Laboratory for Brucella, Munich, Germany
| | - Lothar Zoeller
- Bundeswehr Institute of Microbiology, Munich, Germany
- National Consultant Laboratory for Brucella, Munich, Germany
| | - Sabine Zange
- Bundeswehr Institute of Microbiology, Munich, Germany
- National Consultant Laboratory for Brucella, Munich, Germany
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13
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Lian DS, Zhao SJ. Capillary electrophoresis based on nucleic acid detection for diagnosing human infectious disease. Clin Chem Lab Med 2017; 54:707-38. [PMID: 26352354 DOI: 10.1515/cclm-2015-0096] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 06/17/2015] [Indexed: 01/22/2023]
Abstract
Rapid transmission, high morbidity, and mortality are the features of human infectious diseases caused by microorganisms, such as bacteria, fungi, and viruses. These diseases may lead within a short period of time to great personal and property losses, especially in regions where sanitation is poor. Thus, rapid diagnoses are vital for the prevention and therapeutic intervention of human infectious diseases. Several conventional methods are often used to diagnose infectious diseases, e.g. methods based on cultures or morphology, or biochemical tests based on metabonomics. Although traditional methods are considered gold standards and are used most frequently, they are laborious, time consuming, and tedious and cannot meet the demand for rapid diagnoses. Disease diagnosis using capillary electrophoresis methods has the advantages of high efficiency, high throughput, and high speed, and coupled with the different nucleic acid detection strategies overcomes the drawbacks of traditional identification methods, precluding many types of false positive and negative results. Therefore, this review focuses on the application of capillary electrophoresis based on nucleic detection to the diagnosis of human infectious diseases, and offers an introduction to the limitations, advantages, and future developments of this approach.
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14
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Sankarasubramanian J, Vishnu US, Gunasekaran P, Rajendhran J. A genome-wide SNP-based phylogenetic analysis distinguishes different biovars of Brucella suis. INFECTION GENETICS AND EVOLUTION 2016; 41:213-217. [PMID: 27085292 DOI: 10.1016/j.meegid.2016.04.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 04/08/2016] [Accepted: 04/11/2016] [Indexed: 01/08/2023]
Abstract
Brucellosis is an important zoonotic disease caused by Brucella spp. Brucella suis is the etiological agent of porcine brucellosis. B. suis is the most genetically diverged species within the genus Brucella. We present the first large-scale B. suis phylogenetic analysis based on an alignment-free k-mer approach of gathering polymorphic sites from whole genome sequences. Genome-wide core-SNP based phylogenetic tree clearly differentiated and discriminated the B. suis biovars and the vaccine strain into different clades. A total of 16,756 SNPs were identified from the genome sequences of 54 B. suis strains. Also, biovar-specific SNPs were identified. The vaccine strain B. suis S2-30 is extensively used in China, which was discriminated from all biovars with the accumulation of the highest number of SNPs. We have also identified the SNPs between B. suis vaccine strain S2-30 and its closest homolog, B. suis biovar 513UK. The highest number of mutations (22) was observed in the phosphomannomutase (pmm) gene essential for the synthesis of O-antigen. Also, mutations were identified in several virulent genes including genes coding for type IV secretion system and the effector proteins, which could be responsible for the attenuated virulence of B. suis S2-30.
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Affiliation(s)
- Jagadesan Sankarasubramanian
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India
| | - Udayakumar S Vishnu
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India
| | - Paramasamy Gunasekaran
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India
| | - Jeyaprakash Rajendhran
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India.
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15
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Piranfar V, Sharif M, Hashemi M, Vahdati AR, Mirnejad R. Detection and discrimination of two Brucella species by multiplex real-time PCR and high-resolution melt analysis curve from human blood and comparison of results using RFLP. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2015; 18:909-14. [PMID: 26523223 PMCID: PMC4620191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
OBJECTIVES Rapid and accurate detection of Brucella abortus and Brucella melitensis from clinical samples is so important because antibiotic treatment has major side effects. This study reveals a new method in detection of clinical samples of brucellosis using real-time PCR and high-resolution melt (HRM) curve analysis. MATERIALS AND METHODS 160 brucellosis suspicious samples with more than 1/80 serum antibody titers were collected and the results were compared with the RFLP method. In order to amplify the sequences for HRM analysis, vdcc, int-hyp and glk and for RFLP, omp2a and omp2b with PstI and Hinf1 restriction endonuclease were used. At last, the accuracy and specificity of the two methods were compared with each other. RESULTS Out of these 160 samples, multiplex real time PCR showed 108 positive samples (67.5%), including 56% B. melitensis and 44% B. abortus; whereas in PCR-RFLP 52 out of 160 samples were positive, where recognition of two species were accordant with HRM analysis, separation was based on the size of the amplified fragment. Using the designed primers and performing the assay, we confirmed this method to be much faster and have lower cost with more than 99% accuracy compared to methods such as RFLP. CONCLUSION The present study showed that this technique, which scans gene segments and creates an analysis pattern for detection of clinical samples, is useful and more dominant compared with PCR-RFLP. Thus, this method can be used for brucellosis detection, and clinical and epidemiological research.
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Affiliation(s)
- Vahhab Piranfar
- Department of Biology, Tonekabon Branch, Islamic Azad University of Tonekabon, Tonekabon, Iran
| | - Malike Sharif
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mojtaba Hashemi
- Department of Biology, Tonekabon Branch, Islamic Azad University of Tonekabon, Tonekabon, Iran
| | - Ali Reza Vahdati
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Reza Mirnejad
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran,Corresponding author: Reza Mirnejad. Molecular Biology Research Center, Baqiyatallah University Medical of Sciences Tehran, Iran. Tel: +98-21-82482554; ;
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16
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Tan KK, Tan YC, Chang LY, Lee KW, Nore SS, Yee WY, Mat Isa MN, Jafar FL, Hoh CC, AbuBakar S. Full genome SNP-based phylogenetic analysis reveals the origin and global spread of Brucella melitensis. BMC Genomics 2015; 16:93. [PMID: 25888205 PMCID: PMC4409723 DOI: 10.1186/s12864-015-1294-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Accepted: 01/29/2015] [Indexed: 11/17/2022] Open
Abstract
Background Brucellosis is an important zoonotic disease that affects both humans and animals. We sequenced the full genome and characterised the genetic diversity of two Brucella melitensis isolates from Malaysia and the Philippines. In addition, we performed a comparative whole-genome single nucleotide polymorphism (SNP) analysis of B. melitensis strains collected from around the world, to investigate the potential origin and the history of the global spread of B. melitensis. Results Single sequencing runs of each genome resulted in draft genome sequences of MY1483/09 and Phil1136/12, which covered 99.85% and 99.92% of the complete genome sequences, respectively. The B. melitensis genome sequences, and two B. abortus strains used as the outgroup strains, yielded a total of 13,728 SNP sites. Phylogenetic analysis using whole-genome SNPs and geographical distribution of the isolates revealed spatial clustering of the B. melitensis isolates into five genotypes, I, II, III, IV and V. The Mediterranean strains, identified as genotype I, occupied the basal node of the phylogenetic tree, suggesting that B. melitensis may have originated from the Mediterranean regions. All of the Asian B. melitensis strains clustered into genotype II with the SEA strains, including the two isolates sequenced in this study, forming a distinct clade denoted here as genotype IId. Genotypes III, IV and V of B. melitensis demonstrated a restricted geographical distribution, with genotype III representing the African lineage, genotype IV representing the European lineage and genotype V representing the American lineage. Conclusion We showed that SNPs retrieved from the B. melitensis draft full genomes were sufficient to resolve the interspecies relationships between B. melitensis strains and to discriminate between the vaccine and endemic strains. Phylogeographic reconstruction of the history of B. melitensis global spread at a finer scale by using whole-genome SNP analyses supported the origin of all B. melitensis strains from the Mediterranean region. The possible global distribution of B. melitensis following the ancient trade routes was also consistent with whole-genome SNP phylogeny. The whole genome SNP phylogenetics analysis, hence is a powerful tool for intraspecies discrimination of closely related species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1294-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kim-Kee Tan
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603, Kuala Lumpur, Malaysia. .,Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Yung-Chie Tan
- Codon Genomics S/B, No 26, Jalan Dutamas 7, Taman Dutamas, Balakong, 43200, Seri Kembangan, Selangor, Malaysia.
| | - Li-Yen Chang
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603, Kuala Lumpur, Malaysia. .,Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Kok Wei Lee
- Codon Genomics S/B, No 26, Jalan Dutamas 7, Taman Dutamas, Balakong, 43200, Seri Kembangan, Selangor, Malaysia.
| | - Siti Sarah Nore
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Wai-Yan Yee
- Codon Genomics S/B, No 26, Jalan Dutamas 7, Taman Dutamas, Balakong, 43200, Seri Kembangan, Selangor, Malaysia.
| | - Mohd Noor Mat Isa
- Malaysia Genome Institute, Ministry of Science, Technology and Innovation, Jalan Bangi, 43000, Kajang, Selangor, Malaysia.
| | - Faizatul Lela Jafar
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Chee-Choong Hoh
- Codon Genomics S/B, No 26, Jalan Dutamas 7, Taman Dutamas, Balakong, 43200, Seri Kembangan, Selangor, Malaysia.
| | - Sazaly AbuBakar
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603, Kuala Lumpur, Malaysia. .,Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
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Moreno E. Retrospective and prospective perspectives on zoonotic brucellosis. Front Microbiol 2014; 5:213. [PMID: 24860561 PMCID: PMC4026726 DOI: 10.3389/fmicb.2014.00213] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Accepted: 04/23/2014] [Indexed: 11/13/2022] Open
Abstract
Members of the genus Brucella are pathogenic bacteria exceedingly well adapted to their hosts. The bacterium is transmitted by direct contact within the same host species or accidentally to secondary hosts, such as humans. Human brucellosis is strongly linked to the management of domesticated animals and ingestion of their products. Since the domestication of ungulates and dogs in the Fertile Crescent and Asia in 12000 and 33000 ya, respectively, a steady supply of well adapted emergent Brucella pathogens causing zoonotic disease has been provided. Likewise, anthropogenic modification of wild life may have also impacted host susceptibility and Brucella selection. Domestication and human influence on wild life animals are not neutral phenomena. Consequently, Brucella organisms have followed their hosts’ fate and have been selected under conditions that favor high transmission rate. The “arm race” between Brucella and their preferred hosts has been driven by genetic adaptation of the bacterium confronted with the evolving immune defenses of the host. Management conditions, such as clustering, selection, culling, and vaccination of Brucella preferred hosts have profound influences in the outcome of brucellosis and in the selection of Brucella organisms. Countries that have controlled brucellosis systematically used reliable smooth live vaccines, consistent immunization protocols, adequate diagnostic tests, broad vaccination coverage and sustained removal of the infected animals. To ignore and misuse tools and strategies already available for the control of brucellosis may promote the emergence of new Brucella variants. The unrestricted use of low-efficacy vaccines may promote a “false sense of security” and works towards selection of Brucella with higher virulence and transmission potential.
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Affiliation(s)
- Edgardo Moreno
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional Heredia, Costa Rica ; Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica San José, Costa Rica
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