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Zhang Y, Lyu Y, Wang D, Feng M, Shen S, Zhu L, Pan C, Zai X, Wang S, Guo Y, Yu S, Gong X, Chen Q, Wang H, Wang Y, Liu X. Rapid Identification of Brucella Genus and Species In Silico and On-Site Using Novel Probes with CRISPR/Cas12a. Microorganisms 2024; 12:1018. [PMID: 38792847 PMCID: PMC11124060 DOI: 10.3390/microorganisms12051018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/23/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Human brucellosis caused by Brucella is a widespread zoonosis that is prevalent in many countries globally. The high homology between members of the Brucella genus and Ochrobactrum spp. often complicates the determination of disease etiology in patients. The efficient and reliable identification and distinction of Brucella are of primary interest for both medical surveillance and outbreak purposes. A large amount of genomic data for the Brucella genus was analyzed to uncover novel probes containing single-nucleotide polymorphisms (SNPs). GAMOSCE v1.0 software was developed based on the above novel eProbes. In conjunction with clinical requirements, an RPA-Cas12a detection method was developed for the on-site determination of B. abortus and B. melitensis by fluorescence and lateral flow dipsticks (LFDs). We demonstrated the potential of these probes for rapid and accurate detection of the Brucella genus and five significant Brucella species in silico using GAMOSCE. GAMOSCE was validated on different Brucella datasets and correctly identified all Brucella strains, demonstrating a strong discrimination ability. The RPA-Cas12a detection method showed good performance in detection in clinical blood samples and veterinary isolates. We provide both in silico and on-site methods that are convenient and reliable for use in local hospitals and public health programs for the detection of brucellosis.
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Affiliation(s)
- Yan Zhang
- College of Food Science and Technology, Shanghai Ocean University, 999 Hucheng Huan Road, Lingang New City, Shanghai 201306, China
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Yufei Lyu
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China
- Laboratory of Advanced Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Dongshu Wang
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Meijie Feng
- College of Food Science and Technology, Shanghai Ocean University, 999 Hucheng Huan Road, Lingang New City, Shanghai 201306, China
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Sicheng Shen
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Li Zhu
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Chao Pan
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Xiaodong Zai
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Shuyi Wang
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Yan Guo
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Shujuan Yu
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Xiaowei Gong
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Chengguan District, Lanzhou 730046, China
| | - Qiwei Chen
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Chengguan District, Lanzhou 730046, China
| | - Hengliang Wang
- College of Food Science and Technology, Shanghai Ocean University, 999 Hucheng Huan Road, Lingang New City, Shanghai 201306, China
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China
- Laboratory of Advanced Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Yuanzhi Wang
- School of Medicine, Shihezi University, Xinjiang Uygur Autonomous Region, Shihezi 832002, China
| | - Xiankai Liu
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China
- Laboratory of Advanced Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China
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Thompson JE. Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry in veterinary medicine: Recent advances (2019-present). Vet World 2022; 15:2623-2657. [PMID: 36590115 PMCID: PMC9798047 DOI: 10.14202/vetworld.2022.2623-2657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/11/2022] [Indexed: 11/22/2022] Open
Abstract
Matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) mass spectrometry (MS) has become a valuable laboratory tool for rapid diagnostics, research, and exploration in veterinary medicine. While instrument acquisition costs are high for the technology, cost per sample is very low, the method requires minimal sample preparation, and analysis is easily conducted by end-users requiring minimal training. Matrix-assisted laser desorption ionization-time-of-flight MS has found widespread application for the rapid identification of microorganisms, diagnosis of dermatophytes and parasites, protein/lipid profiling, molecular diagnostics, and the technique demonstrates significant promise for 2D chemical mapping of tissue sections collected postmortem. In this review, an overview of the MALDI-TOF technique will be reported and manuscripts outlining current uses of the technology for veterinary science since 2019 will be summarized. The article concludes by discussing gaps in knowledge and areas of future growth.
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Affiliation(s)
- Jonathan E. Thompson
- School of Veterinary Medicine, Texas Tech University, Amarillo, Texas 79106, United States,Corresponding author: Jonathan E. Thompson, e-mail:
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Lopes CE, De Carli S, Feltes BC, Pinto ÉSM, Sala RDV, Dorn M, Siqueira FM. Genetic and molecular Omp25 analyses from worldwide Brucella canis strains: Possible mutational influences in protein function. Gene 2022; 817:146175. [PMID: 35031422 DOI: 10.1016/j.gene.2021.146175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/12/2021] [Accepted: 12/06/2021] [Indexed: 11/22/2022]
Abstract
Brucella canis is responsible for canine brucellosis, a neglected zoonotic disease. The omp25 gene has been described as an important marker for Brucella intra-species differentiation, in addition to the ability to interact with the host immune system. Therefore, this study investigated the omp25 sequence from B. canis strains associated to a phylogenetic characterization and the unveiling of the molecular structure. In vitro analyses comprised DNA extraction, PCR, and sequencing of omp25 from 19 B. canis strains. Moreover, in silico analyses were performed at nucleotide level for phylogenetic characterization and evolutionary history of B. canis omp25 gene; and in amino acid level including modeling, dynamics, and epitope prediction of B. canis Omp25 protein. Here, we identified a new mutation, L109P, which diverges the worldwide omp25 sequences in two large branches. Interestingly, this mutation appears to have epidemiology importance, based on a geographical distribution of B. canis strains. Structural and molecular dynamics analyses of Omp25 revealed that Omp25L109P does not sustain its native β-barrel. Likewise, the conformation of B-cell epitope on the mutated region was changed in Omp25L109P protein. Even without an evolutive marker, the new identified mutation appears to affect the basic function of B. canis Omp25 protein, which could indicate virulence adaptation for some B. canis strains in a context of geographical disposition.
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Affiliation(s)
- Cassiane Elisabete Lopes
- Laboratory of Veterinary Bacteriology, Veterinary School, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil; Programa de Pós-Graduação em Ciências Veterinárias, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Silvia De Carli
- Laboratory of Veterinary Bacteriology, Veterinary School, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil; Programa de Pós-Graduação em Ciências Veterinárias, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Bruno César Feltes
- Structural Bioinformatics and Computational Biology Laboratory, Institute of Informatics, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil; Department of Genetics, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil; Department of Biophysics, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Éderson Sales Moreira Pinto
- Structural Bioinformatics and Computational Biology Laboratory, Institute of Informatics, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil; Center of Biotechnology, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Rafaella Dalla Vecchia Sala
- Laboratory of Veterinary Bacteriology, Veterinary School, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Márcio Dorn
- Structural Bioinformatics and Computational Biology Laboratory, Institute of Informatics, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil; National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil; Center of Biotechnology, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Franciele Maboni Siqueira
- Laboratory of Veterinary Bacteriology, Veterinary School, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil; Programa de Pós-Graduação em Ciências Veterinárias, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.
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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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Halabian R, Valizadeh Arshad, Ahmadi A, Saeedi P, Azimzadeh Jamalkandi S, Alivand MR. Laboratory methods to decipher epigenetic signatures: a comparative review. Cell Mol Biol Lett 2021; 26:46. [PMID: 34763654 PMCID: PMC8582164 DOI: 10.1186/s11658-021-00290-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 10/28/2021] [Indexed: 12/15/2022] Open
Abstract
Epigenetics refers to nucleotide sequence-independent events, and heritable changes, including DNA methylation and histone modification (as the two main processes), contributing to the phenotypic features of the cell. Both genetics and epigenetics contribute to determining the outcome of regulatory gene expression systems. Indeed, the flexibility of epigenetic effects and stability of genetic coding lead to gene regulation complexity in response signals. Since some epigenetic changes are significant in abnormalities such as cancers and neurodegenerative diseases, the initial changes, dynamic and reversible properties, and diagnostic potential of epigenomic phenomena are subject to epigenome-wide association studies (EWAS) for therapeutic aims. Based on recent studies, methodological developments are necessary to improve epigenetic research. As a result, several methods have been developed to explore epigenetic alterations at low, medium, and high scales, focusing on DNA methylation and histone modification detection. In this research field, bisulfite-, enzyme sensitivity- and antibody specificity-based techniques are used for DNA methylation, whereas histone modifications are gained based on antibody recognition. This review provides a mechanism-based understanding and comparative overview of the most common techniques for detecting the status of epigenetic effects, including DNA methylation and histone modifications, for applicable approaches from low- to high-throughput scales.
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Affiliation(s)
- Raheleh Halabian
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Valizadeh Arshad
- Department of Stem Cell and Developmental Biology, Cell Science Research Center, Royan Institute For Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Ali Ahmadi
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Pardis Saeedi
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Sadegh Azimzadeh Jamalkandi
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Mollasadra Ave., 14359-16471, Tehran, Iran.
| | - Mohammad Reza Alivand
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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Kornspan D, Brendebach H, Hofreuter D, Mathur S, Blum SE, Fleker M, Bardenstein S, Al Dahouk S. Protein Biomarker Identification for the Discrimination of Brucella melitensis Field Isolates From the Brucella melitensis Rev.1 Vaccine Strain by MALDI-TOF MS. Front Microbiol 2021; 12:712601. [PMID: 34745025 PMCID: PMC8569450 DOI: 10.3389/fmicb.2021.712601] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 09/27/2021] [Indexed: 11/13/2022] Open
Abstract
Brucella melitensis Rev.1 is a live attenuated vaccine strain that is widely used to control brucellosis in small ruminants. For successful surveillance and control programs, rapid identification and characterization of Brucella isolates and reliable differentiation of vaccinated and naturally infected animals are essential prerequisites. Although MALDI-TOF MS is increasingly applied in clinical microbiology laboratories for the diagnosis of brucellosis, species or even strain differentiation by this method remains a challenge. To detect biomarkers, which enable to distinguish the B. melitensis Rev.1 vaccine strain from B. melitensis field isolates, we initially searched for unique marker proteins by in silico comparison of the B. melitensis Rev.1 and 16M proteomes. We found 113 protein sequences of B. melitensis 16M that revealed a homologous sequence in the B. melitensis Rev.1 annotation and 17 of these sequences yielded potential biomarker pairs. MALDI-TOF MS spectra of 18 B. melitensis Rev.1 vaccine and 183 Israeli B. melitensis field isolates were subsequently analyzed to validate the identified marker candidates. This approach detected two genus-wide unique biomarkers with properties most similar to the ribosomal proteins L24 and S12. These two proteins clearly discriminated B. melitensis Rev.1 from the closely related B. melitensis 16M and the Israeli B. melitensis field isolates. In addition, we verified their discriminatory power using a set of B. melitensis strains from various origins and of different MLVA types. Based on our results, we propose MALDI-TOF MS profiling as a rapid, cost-effective alternative to the traditional, time-consuming approach to differentiate certain B. melitensis isolates on strain level.
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Affiliation(s)
- David Kornspan
- Department of Bacteriology, Kimron Veterinary Institute (KVI), Bet Dagan, Israel
| | - Holger Brendebach
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Dirk Hofreuter
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Shubham Mathur
- Department of Bacteriology, Kimron Veterinary Institute (KVI), Bet Dagan, Israel
| | - Shlomo Eduardo Blum
- Department of Bacteriology, Kimron Veterinary Institute (KVI), Bet Dagan, Israel
| | - Marcelo Fleker
- Department of Bacteriology, Kimron Veterinary Institute (KVI), Bet Dagan, Israel
| | | | - Sascha Al Dahouk
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
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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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Canine brucellosis in Costa Rica reveals widespread Brucella canis infection and the recent introduction of foreign strains. Vet Microbiol 2021; 257:109072. [PMID: 33965789 DOI: 10.1016/j.vetmic.2021.109072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/13/2021] [Indexed: 01/31/2023]
Abstract
Brucellosis is a prevalent disease in Costa Rica (CR), with an increasing number of human infections. Close to half of homes in CR have one or more dogs, corresponding to ∼1.4 million canines, most of them in the Central Valley within or near the cities of San José, Heredia, and Alajuela. From 302 dog sera collected from this region, 19 were positive for Brucella canis antigens, and five had antibodies against smooth lipopolysaccharide, suggesting infections by both B. canis and other Brucella species. B. canis strains were isolated in the Central Valley from 26 kennel dogs and three pet dogs, all displaying clinical signs of canine brucellosis. We detected three recent introductions of different B. canis strains in kennels: two traced from Mexico and one from Panama. Multiple locus-variable number tandem repeats (MLVA-16) and whole-genome sequencing (WGSA) analyses showed that B. canis CR strains comprise three main lineages. The tree topologies obtained by WGSA and MLVA-16 just partially agreed, indicating that the latter analysis is not suitable for phylogenetic studies. The fatty acid methyl ester analysis resolved five different B. canis groups, showing less resolution power than the MLVA-16 and WGSA. Lactobacillic acid was absent in linages I and II but present in linage III, supporting the recent introductions of B. canis strains from Mexico. B. canis displaying putative functional cyclopropane synthase for the synthesis of lactobacillic acid are phylogenetically intertwined with B. canis with non-functional protein, indicating that mutations have occurred independently in the various lineages.
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