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Akar K, Holzer K, Hoelzle LE, Yıldız Öz G, Abdelmegid S, Baklan EA, Eroğlu B, Atıl E, Moustafa SA, Wareth G, Elkhayat M. An Evaluation of the Lineage of Brucella Isolates in Turkey by a Whole-Genome Single-Nucleotide Polymorphism Analysis. Vet Sci 2024; 11:316. [PMID: 39058000 PMCID: PMC11281417 DOI: 10.3390/vetsci11070316] [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: 05/30/2024] [Revised: 07/11/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
Brucellosis is a disease caused by the Brucella (B.) species. It is a zoonotic disease that affects farm animals and causes economic losses in many countries worldwide. Brucella has the ability to persist in the environment and infect the host at low doses. Thus, it is more important to trace brucellosis outbreaks, identify their sources of infection, and interrupt their transmission. Some countries already have initial data, but most of these data are based on a Multiple-Locus Variable-Number Tandem-Repeat Analysis (MLVA), which is completely unsuitable for studying the Brucella genome. Since brucellosis is an endemic disease in Turkey, this study aimed to examine the genome of Turkish Brucella isolates collected between 2018 and 2020, except for one isolate, which was from 2012. A total of 28 strains of B. melitensis (n = 15) and B. abortus (n = 13) were analyzed using a core-genome single-nucleotide polymorphism (cgSNP) analysis. A potential connection between the Turkish isolates and entries from Sweden, Israel, Syria, Austria, and India for B. melitensis was detected. For B. abortus, there may be potential associations with entries from China. This explains the tight ties found between Brucella strains from neighboring countries and isolates from Turkey. Therefore, it is recommended that strict measures be taken and the possible effects of uncontrolled animal introduction are emphasized.
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Affiliation(s)
- Kadir Akar
- Faculty of Veterinary Medicine, Van Yuzuncu Yıl University, 65090 Van, Turkey
| | - Katharina Holzer
- Department of Livestock Infectiology and Environmental Hygiene, Institute of Animal Science, University of Hohenheim, 70599 Stuttgart, Germany;
| | - Ludwig E. Hoelzle
- Department of Livestock Infectiology and Environmental Hygiene, Institute of Animal Science, University of Hohenheim, 70599 Stuttgart, Germany;
| | - Gülseren Yıldız Öz
- NRL for Brucellosis, Pendik Veterinary Control Institute, 34890 Istanbul, Turkey; (G.Y.Ö.); (E.A.B.); (B.E.); (E.A.)
| | | | - Emin Ayhan Baklan
- NRL for Brucellosis, Pendik Veterinary Control Institute, 34890 Istanbul, Turkey; (G.Y.Ö.); (E.A.B.); (B.E.); (E.A.)
| | - Buket Eroğlu
- NRL for Brucellosis, Pendik Veterinary Control Institute, 34890 Istanbul, Turkey; (G.Y.Ö.); (E.A.B.); (B.E.); (E.A.)
| | - Eray Atıl
- NRL for Brucellosis, Pendik Veterinary Control Institute, 34890 Istanbul, Turkey; (G.Y.Ö.); (E.A.B.); (B.E.); (E.A.)
| | - Shawky A. Moustafa
- Faculty of Veterinary Medicine, Benha University, Toukh 13736, Egypt; (S.A.M.); (M.E.)
| | - Gamal Wareth
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, 07743 Jena, Germany;
- Institute of Infectious Diseases and Infection Control, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany
| | - Manar Elkhayat
- Faculty of Veterinary Medicine, Benha University, Toukh 13736, Egypt; (S.A.M.); (M.E.)
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Shevtsov A, Cloeckaert A, Berdimuratova K, Shevtsova E, Shustov AV, Amirgazin A, Karibayev T, Kamalova D, Zygmunt MS, Ramanculov Y, Vergnaud G. Brucella abortus in Kazakhstan, population structure and comparison with worldwide genetic diversity. Front Microbiol 2023; 14:1106994. [PMID: 37032899 PMCID: PMC10073595 DOI: 10.3389/fmicb.2023.1106994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 03/01/2023] [Indexed: 04/11/2023] Open
Abstract
Brucella abortus is the main causative agent of brucellosis in cattle, leading to severe economic consequences in agriculture and affecting public health. The zoonotic nature of the infection increases the need to control the spread and dynamics of outbreaks in animals with the incorporation of high resolution genotyping techniques. Based on such methods, B. abortus is currently divided into three clades, A, B, and C. The latter includes subclades C1 and C2. This study presents the results of whole-genome sequencing of 49 B. abortus strains isolated in Kazakhstan between 1947 and 2015 and of 36 B. abortus strains of various geographic origins isolated from 1940 to 2004. In silico Multiple Locus Sequence Typing (MLST) allowed to assign strains from Kazakhstan to subclades C1 and to a much lower extend C2. Whole-genome Single-Nucleotide Polymorphism (wgSNP) analysis of the 46 strains of subclade C1 with strains of worldwide origins showed clustering with strains from neighboring countries, mostly North Caucasia, Western Russia, but also Siberia, China, and Mongolia. One of the three Kazakhstan strains assigned to subclade C2 matched the B. abortus S19 vaccine strain used in cattle, the other two were genetically close to the 104 M vaccine strain. Bayesian phylodynamic analysis dated the introduction of B. abortus subclade C1 into Kazakhstan to the 19th and early 20th centuries. We discuss this observation in view of the history of population migrations from Russia to the Kazakhstan steppes.
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Affiliation(s)
- Alexandr Shevtsov
- National Center for Biotechnology, Astana, Kazakhstan
- *Correspondence: Alexandr Shevtsov,
| | | | | | | | | | | | | | | | | | - Yerlan Ramanculov
- National Center for Biotechnology, Astana, Kazakhstan
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
| | - Gilles Vergnaud
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
- Gilles Vergnaud,
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Core Genome Multilocus Sequence Typing Scheme for Improved Characterization and Epidemiological Surveillance of Pathogenic Brucella. J Clin Microbiol 2022; 60:e0031122. [PMID: 35852343 PMCID: PMC9387271 DOI: 10.1128/jcm.00311-22] [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] [Indexed: 11/30/2022] Open
Abstract
Brucellosis poses a significant burden to human and animal health worldwide. Robust and harmonized molecular epidemiological approaches and population studies that include routine disease screening are needed to efficiently track the origin and spread of Brucella strains. Core genome multilocus sequence typing (cgMLST) is a powerful genotyping system commonly used to delineate pathogen transmission routes for disease surveillance and control. Except for Brucella melitensis, cgMLST schemes for Brucella species are currently not established. Here, we describe a novel cgMLST scheme that covers multiple Brucella species. We first determined the phylogenetic breadth of the genus using 612 Brucella genomes. We selected 1,764 genes that were particularly well conserved and typeable in at least 98% of these genomes. We tested the new scheme on 600 genomes and found high agreement with the whole-genome-based single nucleotide polymorphism (SNP) analysis. Next, we applied the scheme to reanalyze the genome of Brucella strains from epidemiologically linked outbreaks. We demonstrated the applicability of the new scheme for high-resolution typing required in outbreak investigations as previously reported with whole-genome SNP methods. We also used the novel scheme to define the global population structure of the genus using 1,322 Brucella genomes. Finally, we demonstrated the possibility of tracing distribution of Brucella strains by performing cluster analysis of cgMLST profiles and found nearly identical cgMLST profiles in different countries. Our results show that sequencing depth of more than 40-fold is optimal for allele calling with this scheme. In summary, this study describes a novel Brucella-wide cgMLST scheme that is applicable in Brucella molecular epidemiology and helps in accurately tracking and thus controlling the sources of infection. The scheme is publicly accessible and should represent a valuable resource for laboratories with limited computational resources and bioinformatics expertise.
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Molecular characterization of zoonotic Brucella species isolated from animal and human samples in Iran. Acta Trop 2022; 229:106363. [PMID: 35149040 DOI: 10.1016/j.actatropica.2022.106363] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 01/25/2022] [Accepted: 02/07/2022] [Indexed: 11/20/2022]
Abstract
Brucellosis is an endemic infection in Iran and represents a serious health problem in humans and livestock causing important economic losses. The objective of this study was to undertake molecular characterization of Brucella spp. isolated from humans and livestock in several provinces of Iran including by multi-locus sequence typing (MLST), in order to understand the genotypes circulating in Iran and their relationship to genotypes globally. A total of 23 Brucella isolates were isolated from eight milk samples (seven cows, and one camel), human blood samples (seven), bovine lymph nodes (two), and samples from aborted fetuses (three sheep, two cows, and one goat). Phenotypic and molecular identification of Brucella isolates was performed on all isolated bacteria and showed that all were either Brucella melitensis or Brucella abortus. B. melitensis was associated with ovine/caprine and camel samples, most human isolates, and a significant minority of cattle isolates. In contrast B. abortus from livestock was associated only with isolations from bovine samples, as well as a single human sample. These results indicate that both B. melitensis and B. abortus contribute to the human brucellosis burden in Iran. B. melitensis isolates comprised three MLST-9 genotypes, the common and globally distributed ST8, a single representative of ST7, and several additional examples of ST102, a genotype previously only reported in a single isolate from a human brucellosis case believed to be acquired through travel to Iran. B. abortus isolates represented two globally common MLST-9 genotypes (ST1 and ST2), with relationships to biotype and other PCR-based typing methods consistent with previous observations. The results provide the basis for further studies examining the molecular epidemiology of Brucella circulating in Iran and the relationships of local isolates to those present globally.
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An CH, Nie SM, Sun YX, Fan SP, Luo BY, Li Z, Liu ZG, Chang WH. Seroprevalence trend of human brucellosis and MLVA genotyping characteristics of Brucella melitensis in Shaanxi Province, China, during 2008-2020. Transbound Emerg Dis 2021; 69:e423-e434. [PMID: 34510783 DOI: 10.1111/tbed.14320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/25/2021] [Accepted: 09/08/2021] [Indexed: 11/29/2022]
Abstract
In this study, a total of 179,907 blood samples from populations with suspected Brucella spp. infections were collected between 2008 and 2020 and analyzed by the Rose Bengal plate test (RBPT) and serum agglutination test (SAT). Moreover, conventional biotyping, B. abortus-melitensis-ovis-suis polymerase chain reaction (AMOS-PCR), and multiple-locus variable-number tandem repeat analysis (MLVA) was applied to characterize the isolated strains. A total of 8103 (4.50%) samples were positive in RBPT, while 7705 (4.28%, 95% confidence interval (CI) 4.19-4.37) samples were positive in SAT. There was a significant difference in seroprevalence for human brucellosis over time, in different areas and different cities (districts) (χ2 = 2 = 32.23, 1984.14, and 3749.51, p < .05). The highest seropositivity (8.22% (4, 965/60393; 95% CI 8.00-8.44) was observed in Yulin City, which borders Inner Mongolia, Ningxia, and Gansu Province, China, regions that have a high incidence of human brucellosis. Moreover, 174 Brucella strains were obtained, including nine with B. melitensis bv. 1, 145 with B. melitensis bv. 3, and 20 with B. melitensis variants. After random selection, 132 B. melitensis were further genotyped using MLVA-16. The 132 strains were sorted into 100 MLVA-16 genotypes (GTs) (GT 1-100), 81 of which were single GTs represented by singular independent strains. The remaining 19 shared GTs involved 51 strains, and each GT included two to seven isolates from the Shaan northern and Guanzhong areas. These data indicated that although sporadic cases were a dominant epidemic characteristic of human brucellosis in this province, more than 38.6% (51/132) outbreaks were also found in the Shaan northern area and Guanzhong areas. The 47 shared MLVA-16 GTs were observed in strains (n = 71) from this study and strains (n = 337) from 19 other provinces of China. These data suggest that strains from the northern provinces are a potential source of human brucellosis cases in Shaanxi Province. It is urgent to strengthen the surveillance and control of the trade and transfer of infected sheep among regions.
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Affiliation(s)
- Cui-Hong An
- Department of Plague and Brucellosis, Shaanxi Center for Disease Control and Prevention, Xi'an, China.,Department of Microbiology and Immunology, School of Medicine, Xi'an Jiaotong University, Xi'an, China
| | - Shou-Min Nie
- Department of Plague and Brucellosis, Shaanxi Center for Disease Control and Prevention, Xi'an, China
| | - Yang-Xin Sun
- Department of Plague and Brucellosis, Shaanxi Center for Disease Control and Prevention, Xi'an, China
| | - Suo-Ping Fan
- Department of Plague and Brucellosis, Shaanxi Center for Disease Control and Prevention, Xi'an, China
| | - Bo-Yan Luo
- Department of Plague and Brucellosis, Shaanxi Center for Disease Control and Prevention, Xi'an, China
| | - Zhenjun Li
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Diseases Control and Prevention, Beijing, China
| | - Zhi-Guo Liu
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Diseases Control and Prevention, Beijing, China
| | - Wen-Hui Chang
- Department of Plague and Brucellosis, Shaanxi Center for Disease Control and Prevention, Xi'an, China
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Whole-Genome Sequencing for Tracing the Genetic Diversity of Brucella abortus and Brucella melitensis Isolated from Livestock in Egypt. Pathogens 2021; 10:pathogens10060759. [PMID: 34208761 PMCID: PMC8235727 DOI: 10.3390/pathogens10060759] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/07/2021] [Accepted: 06/11/2021] [Indexed: 02/03/2023] Open
Abstract
Brucellosis is a highly contagious zoonosis that occurs worldwide. Whole-genome sequencing (WGS) has become a widely accepted molecular typing method for outbreak tracing and genomic epidemiology of brucellosis. Twenty-nine Brucella spp. (eight B. abortus biovar 1 and 21 B. melitensis biovar 3) were isolated from lymph nodes, milk, and fetal abomasal contents of infected cattle, buffaloes, sheep, and goats originating from nine districts in Egypt. The isolates were identified by microbiological methods and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Differentiation and genotyping were confirmed using multiplex PCR. Illumina MiSeq® was used to sequence the 29 Brucella isolates. Using MLST typing, ST11 and ST1 were identified among B. melitensis and B. abortus, respectively. Brucella abortus and B. melitensis isolates were divided into two main clusters (clusters 1 and 2) containing two and nine distinct genotypes by core-genome SNP analysis, respectively. The genotypes were irregularly distributed over time and space in the study area. Both Egyptian B. abortus and B. melitensis isolates proved to be genomically unique upon comparison with publicly available sequencing from strains of neighboring Mediterranean, African, and Asian countries. The antimicrobial resistance mechanism caused by mutations in rpoB, gyrA, and gyrB genes associated with rifampicin and ciprofloxacin resistance were identified. To the best of our knowledge, this is the first study investigating the epidemiology of Brucella isolates from livestock belonging to different localities in Egypt based on whole genome analysis.
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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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O'Callaghan D. Human brucellosis: recent advances and future challenges. Infect Dis Poverty 2020; 9:101. [PMID: 32703319 PMCID: PMC7376320 DOI: 10.1186/s40249-020-00715-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 07/03/2020] [Indexed: 11/10/2022] Open
Affiliation(s)
- David O'Callaghan
- Bacterial Virulence and Infectious Disease, University of Montpellier, INSERM, Nimes, France. .,Brucellosis National Reference Centre (CNR), Microbiology Laboratory, Caremeau University Hospital, Nimes, France.
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