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Papić B, Kušar D, Krt B, Ocepek M, Avberšek J. Phylogeography of Brucella suis biovar 2 with focus on Slovenian wildlife. Vet Microbiol 2023; 282:109751. [PMID: 37104938 DOI: 10.1016/j.vetmic.2023.109751] [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: 12/19/2022] [Revised: 04/19/2023] [Accepted: 04/22/2023] [Indexed: 04/29/2023]
Abstract
Brucella suis commonly infects swine but occasionally also other animal species and humans. Wild boars are the most important reservoir of B. suis biovar 2, continually infecting susceptible hosts through close contact. Nevertheless, the genetic diversity of B. suis in wildlife remains understudied. Here, we typed 17 Slovenian B. suis biovar 2 isolates obtained in 2017-2019 from wild boars (n = 16) and a hare (n = 1) using whole-genome sequencing (WGS). To assess the global phylogenetic diversity of B. suis, we compared them to 126 publicly available B. suis genomes. All Slovenian isolates fell within the biovar 2 lineage, confirming the previous multiplex PCR typing results. According to MLST-21, the wild boar isolates were of sequence types (STs) ST16 (n = 8) and ST153 (n = 8); the maximum genetic distance between isolates of the same ST was 28 wgMLST alleles. The ST153 isolates were restricted to the Slovenian-Croatian border and clustered together with the Croatian ST153 isolates from swine, indicating cross-border transmission of B. suis ST153 strain. The hare isolate was of ST40 and was genetically distant (≥ 489 alleles) from the wild boar isolates. The genome-wide phylogeny clearly separated different B. suis biovars. The present study is the first report on the population structure of B. suis in wildlife in Slovenia and shows that the Slovenian B. suis population is genetically heterogeneous. At the species level, B. suis biovars are clearly separated in the WGS-based phylogenetic tree and can therefore be reliably predicted using WGS.
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Affiliation(s)
- Bojan Papić
- University of Ljubljana, Veterinary Faculty, Institute of Microbiology and Parasitology, Gerbičeva 60, 1000 Ljubljana, Slovenia.
| | - Darja Kušar
- University of Ljubljana, Veterinary Faculty, Institute of Microbiology and Parasitology, Gerbičeva 60, 1000 Ljubljana, Slovenia
| | - Brane Krt
- University of Ljubljana, Veterinary Faculty, Institute of Microbiology and Parasitology, Gerbičeva 60, 1000 Ljubljana, Slovenia
| | - Matjaž Ocepek
- University of Ljubljana, Veterinary Faculty, Institute of Microbiology and Parasitology, Gerbičeva 60, 1000 Ljubljana, Slovenia
| | - Jana Avberšek
- University of Ljubljana, Veterinary Faculty, Institute of Microbiology and Parasitology, Gerbičeva 60, 1000 Ljubljana, Slovenia
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2
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Chen Y, Zhu W, Yan T, Chen D, Jiang L, Chen ZH, Wu D. Stomatal morphological variation contributes to global ecological adaptation and diversification of Brassica napus. PLANTA 2022; 256:64. [PMID: 36029339 DOI: 10.1007/s00425-022-03982-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Stomatal density and guard cell length of 274 global core germplasms of rapeseed reveal that the stomatal morphological variation contributes to global ecological adaptation and diversification of Brassica napus. Stomata are microscopic structures of plants for the regulation of CO2 assimilation and transpiration. Stomatal morphology has changed substantially in the adaptation to the external environment during land plant evolution. Brassica napus is a major crop to produce oil, livestock feed and biofuel in the world. However, there are few studies on the regulatory genes controlling stomatal development and their interaction with environmental factors as well as the genetic mechanism of adaptive variation in B. napus. Here, we characterized stomatal density (SD) and guard cell length (GL) of 274 global core germplasms at seedling stage. It was found that among the significant phenotypic variation, European germplasms are mostly winter rapeseed with high stomatal density and small guard cell length. However, the germplasms from Asia (especially China) are semi-winter rapeseed, which is characterized by low stomatal density and large guard cell length. Through selective sweep analysis and homology comparison, we identified several candidate genes related to stomatal density and guard cell length, including Epidermal Patterning Factor2 (EPF2; BnaA09g23140D), Epidermal Patterning Factor Like4 (EPFL4; BnaC01g22890D) and Suppressor of LLP1 (SOL1 BnaC01g22810D). Haplotype and phylogenetic analysis showed that natural variation in EPF2, EPFL4 and SOL1 is closely associated with the winter, spring, and semi-winter rapeseed ecotypes. In summary, this study demonstrated for the first time the relation between stomatal phenotypic variation and ecological adaptation in rapeseed, which is useful for future molecular breeding of rapeseed in the context of evolution and domestication of key stomatal traits and global climate change.
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Affiliation(s)
- Yeke Chen
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China
| | - Weizhuo Zhu
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China
| | - Tao Yan
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Danyi Chen
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China
| | - Lixi Jiang
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW, Australia.
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.
| | - Dezhi Wu
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China.
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China.
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3
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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: 1.0] [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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Gong QL, Sun YH, Yang Y, Zhao B, Wang Q, Li JM, Ge GY, Chen ZY, Shi K, Leng X, Zong Y, Du R. Global Comprehensive Literature Review and Meta-Analysis of Brucella spp. in Swine Based on Publications From 2000 to 2020. Front Vet Sci 2021; 8:630960. [PMID: 34026886 PMCID: PMC8137890 DOI: 10.3389/fvets.2021.630960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Brucellosis, a zoonotic disease, infects various hosts, including swine and humans. It has reemerged in recent years as a public health concern, and current studies on brucellosis infection in swine have been conducted worldwide. However, no meta-analyses of global brucellosis infection in swine have been published. The aim of this study was to provide an overview of Brucella species (spp.) in swine worldwide and the factors associated with its persistence. Results: We searched seven databases for published epidemiological studies on brucellosis in pigs, including the Chinese National Knowledge Infrastructure, Wanfang Data, SpringerLink, ScienceDirect, Web of Science, the VIP Chinese Journal Database and PubMed. We selected 119 articles published from January 1, 2000 to January 3, 2020 for inclusion in the meta-analysis and analyzed the data using a random-effects model. Funnel plots and Egger's test showed significant publication bias in the included studies. The results of the sensitivity analysis showed that our study was relatively stable and reliable. The prevalence of brucellosis in swine was 2.1% (95% CI: 1.6–2.6), of which the highest infection rate, which was found in Europe, was 17.4% (95% CI: 11.1–24.9). The prevalence in feral pigs (15.0%, 95% CI: 8.4–23.2) was higher than that in domestic pigs (1.1%, 95% CI 0.2–2.5). The prevalence in high-income countries (15.7%, 95% CI 8.0–25.3) was significantly higher than that in middle- (0.8%, 95% CI 0.5–1.1), and low-income countries (0.1%, 95% CI 0.0–0.2). The prevalence was highest in finishing pigs at 4.9% (95% CI 0.9–11.0), and lowest among suckling pigs at 0% (95% CI 0.0–0.5). Conclusion: The Brucella prevalence in pig herds currently is distributed widely throughout the world. In some countries, swine brucellosis may be a neglected zoonotic disease. We recommend long-term monitoring of the prevalence of brucellosis in domestic and wild pig herds. Attention should also be paid to animal welfare on intensive pig farms; controlling the breeding density may play an important role in reducing the spread of brucellosis among pigs.
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Affiliation(s)
- Qing-Long Gong
- College of Chinese Medicine Materials, Jilin Agricultural University, Changchun, China.,College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Yu-Han Sun
- College of Chinese Medicine Materials, Jilin Agricultural University, Changchun, China
| | - Yang Yang
- College of Chinese Medicine Materials, Jilin Agricultural University, Changchun, China
| | - Bo Zhao
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Qi Wang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Jian-Ming Li
- College of Chinese Medicine Materials, Jilin Agricultural University, Changchun, China
| | - Gui-Yang Ge
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Zi-Yang Chen
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Kun Shi
- College of Chinese Medicine Materials, Jilin Agricultural University, Changchun, China
| | - Xue Leng
- College of Chinese Medicine Materials, Jilin Agricultural University, Changchun, China
| | - Ying Zong
- College of Chinese Medicine Materials, Jilin Agricultural University, Changchun, China
| | - Rui Du
- College of Chinese Medicine Materials, Jilin Agricultural University, Changchun, China.,Laboratory of Production and Product Application of Sika Deer of Jilin Province, Jilin Agricultural University, Changchun, China.,Key Lab of Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, China
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5
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Zhao ZJ, Li JQ, Ma L, Xue HM, Yang XX, Zhao YB, Qin YM, Yang XW, Piao DR, Zhao HY, Tian GZ, Li Q, Wang JL, Tian G, Jiang H, Xu LQ. Molecular characteristics of Brucella melitensis isolates from humans in Qinghai Province, China. Infect Dis Poverty 2021; 10:42. [PMID: 33771234 PMCID: PMC8004457 DOI: 10.1186/s40249-021-00829-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 03/19/2021] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND The prevalence of human brucellosis in Qinghai Province of China has been increasing rapidly, with confirmed cases distributed across 31 counties. However, the epidemiology of brucellosis transmission has not been fully elucidated. To characterize the infecting strains isolated from humans, multiple-locus variable-number tandem repeats analysis (MLVA) and whole-genome single-nucleotide polymorphism (SNP)-based approaches were employed. METHODS Strains were isolated from two males blood cultures that were confirmed Brucella melitensis positive following biotyping and MLVA. Genomic DNA was extracted from these two strains, and whole-genome sequencing was performed. Next, SNP-based phylogenetic analysis was performed to compare the two strains to 94 B. melitensis strains (complete genome and draft genome) retrieved from online databases. RESULTS The two Brucella isolates were identified as B. melitensis biovar 3 (QH2019001 and QH2019005) following conventional biotyping and were found to have differences in their variable number tandem repeats (VNTRs) using MLVA-16. Phylogenetic examination assigned the 96 strains to five genotype groups, with QH2019001 and QH2019005 assigned to the same group, but different subgroups. Moreover, the QH2019005 strain was assigned to a new subgenotype, IIj, within genotype II. These findings were then combined to determine the geographic origin of the two Brucella strains. CONCLUSIONS Utilizing a whole-genome SNP-based approach enabled differences between the two B. melitensis strains to be more clearly resolved, and facilitated the elucidation of their different evolutionary histories. This approach also revealed that QH2019005 is a member of a new subgenotype (IIj) with an ancient origin in the eastern Mediterranean Sea.
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Affiliation(s)
- Zhi-Jun Zhao
- Qinghai Institute for Endemic Disease Prevention and Control, The department of brucellosis prevention and control, Xining, 810021, Qinghai, China
| | - Ji-Quan Li
- Key Laboratory of Plague Prevention and Research, Qinghai Institute for Endemic Disease Prevention and Control, National Health Commission (2019PT310004) and Key Laboratory for Plague Prevention and Control of Qinghai Province, Xining, 810021, Qinghai, China
| | - Li Ma
- Qinghai Institute for Endemic Disease Prevention and Control, The department of brucellosis prevention and control, Xining, 810021, Qinghai, China
| | - Hong-Mei Xue
- Qinghai Institute for Endemic Disease Prevention and Control, The department of brucellosis prevention and control, Xining, 810021, Qinghai, China
| | - Xu-Xin Yang
- Qinghai Institute for Endemic Disease Prevention and Control, The department of brucellosis prevention and control, Xining, 810021, Qinghai, China
| | - Yuan-Bo Zhao
- Qinghai Institute for Endemic Disease Prevention and Control, The department of brucellosis prevention and control, Xining, 810021, Qinghai, China
| | - Yu-Min Qin
- Qinghai Institute for Endemic Disease Prevention and Control, The department of brucellosis prevention and control, Xining, 810021, Qinghai, China
| | - Xiao-Wen Yang
- 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 Control and Prevention, Beijing, 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 Control and Prevention, Beijing, 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 Control and Prevention, Beijing, China
| | - 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 Control and Prevention, Beijing, China
| | - Qiang Li
- Qinghai Institute for Endemic Disease Prevention and Control, The department of brucellosis prevention and control, Xining, 810021, Qinghai, China
| | - Jian-Ling Wang
- Qinghai Institute for Endemic Disease Prevention and Control, The department of brucellosis prevention and control, Xining, 810021, Qinghai, China
| | - Guang Tian
- Qinghai Institute for Endemic Disease Prevention and Control, The department of brucellosis prevention and control, Xining, 810021, Qinghai, China
| | - Hai Jiang
- Qinghai Institute for Endemic Disease Prevention and Control, The department of brucellosis prevention and control, Xining, 810021, Qinghai, China. .,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 Control and Prevention, Beijing, China.
| | - Li-Qing Xu
- Qinghai Institute for Endemic Disease Prevention and Control, The department of brucellosis prevention and control, Xining, 810021, Qinghai, China.
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Rajendhran J. Genomic insights into Brucella. INFECTION GENETICS AND EVOLUTION 2020; 87:104635. [PMID: 33189905 DOI: 10.1016/j.meegid.2020.104635] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 11/09/2020] [Accepted: 11/11/2020] [Indexed: 01/21/2023]
Abstract
Brucellosis is a zoonotic disease caused by certain species of Brucella. Each species has its preferred host animal, though it can infect other animals too. For a longer period, only six classical species were recognized in the genus Brucella. No vaccine is available for human brucellosis. Therefore, human brucellosis can be controlled only by controlling brucellosis in animals. The genus is now expanding with the newly isolated atypical strains from various animals, including marine mammals. Presently, 12 species of Brucella have been recognized. The first genome of Brucella was released in 2002, and today, we have more than 1500 genomes of Brucella spp. isolated worldwide. Multiple genome sequences are available for the major zoonotic species, B. abortus, B. melitensis, and B. suis. The Brucella genome has two chromosomes with the approximate sizes of 2.1 and 1.2 Mbp. The genome of Brucella is highly conserved across all the species at the nucleotide level. One of the unanswered questions is what makes host preference in different species of Brucella. Here, I summarize the recent advancements in the Brucella genomics research.
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Affiliation(s)
- Jeyaprakash Rajendhran
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India.
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7
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Shakya M, Ahmed SA, Davenport KW, Flynn MC, Lo CC, Chain PSG. Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life. Sci Rep 2020; 10:1723. [PMID: 32015354 PMCID: PMC6997174 DOI: 10.1038/s41598-020-58356-1] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 01/06/2020] [Indexed: 12/02/2022] Open
Abstract
There is growing interest in reconstructing phylogenies from the copious amounts of genome sequencing projects that target related viral, bacterial or eukaryotic organisms. To facilitate the construction of standardized and robust phylogenies for disparate types of projects, we have developed a complete bioinformatic workflow, with a web-based component to perform phylogenetic and molecular evolutionary (PhaME) analysis from sequencing reads, draft assemblies or completed genomes of closely related organisms. Furthermore, the ability to incorporate raw data, including some metagenomic samples containing a target organism (e.g. from clinical samples with suspected infectious agents), shows promise for the rapid phylogenetic characterization of organisms within complex samples without the need for prior assembly.
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Affiliation(s)
- Migun Shakya
- Bioscience Division, Los Alamos National Laboratory, MS-M888, Los Alamos, NM, 87545, USA.
| | - Sanaa A Ahmed
- Bioscience Division, Los Alamos National Laboratory, MS-M888, Los Alamos, NM, 87545, USA
| | - Karen W Davenport
- Bioscience Division, Los Alamos National Laboratory, MS-M888, Los Alamos, NM, 87545, USA
| | - Mark C Flynn
- Bioscience Division, Los Alamos National Laboratory, MS-M888, Los Alamos, NM, 87545, USA
| | - Chien-Chi Lo
- Bioscience Division, Los Alamos National Laboratory, MS-M888, Los Alamos, NM, 87545, USA
| | - Patrick S G Chain
- Bioscience Division, Los Alamos National Laboratory, MS-M888, Los Alamos, NM, 87545, USA.
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Zhou Y, Zhang W, Wu H, Huang K, Jin J. A high-resolution genomic composition-based method with the ability to distinguish similar bacterial organisms. BMC Genomics 2019; 20:754. [PMID: 31638897 PMCID: PMC6805505 DOI: 10.1186/s12864-019-6119-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 09/20/2019] [Indexed: 12/03/2022] Open
Abstract
Background Genomic composition has been found to be species specific and is used to differentiate bacterial species. To date, almost no published composition-based approaches are able to distinguish between most closely related organisms, including intra-genus species and intra-species strains. Thus, it is necessary to develop a novel approach to address this problem. Results Here, we initially determine that the “tetranucleotide-derived z-value Pearson correlation coefficient” (TETRA) approach is representative of other published statistical methods. Then, we devise a novel method called “Tetranucleotide-derived Z-value Manhattan Distance” (TZMD) and compare it with the TETRA approach. Our results show that TZMD reflects the maximal genome difference, while TETRA does not in most conditions, demonstrating in theory that TZMD provides improved resolution. Additionally, our analysis of real data shows that TZMD improves species differentiation and clearly differentiates similar organisms, including similar species belonging to the same genospecies, subspecies and intraspecific strains, most of which cannot be distinguished by TETRA. Furthermore, TZMD is able to determine clonal strains with the TZMD = 0 criterion, which intrinsically encompasses identical composition, high average nucleotide identity and high percentage of shared genomes. Conclusions Our extensive assessment demonstrates that TZMD has high resolution. This study is the first to propose a composition-based method for differentiating bacteria at the strain level and to demonstrate that composition is also strain specific. TZMD is a powerful tool and the first easy-to-use approach for differentiating clonal and non-clonal strains. Therefore, as the first composition-based algorithm for strain typing, TZMD will facilitate bacterial studies in the future.
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Affiliation(s)
- Yizhuang Zhou
- Laboratory of Hepatobiliary and Pancreatic Surgery, The Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, 541001, People's Republic of China. .,Peking-Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, People's Republic of China.
| | - Wenting Zhang
- Laboratory of Hepatobiliary and Pancreatic Surgery, The Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, 541001, People's Republic of China
| | - Huixian Wu
- China-USA Lipids in Health and Disease Research Center, Guilin Medical University, Guilin, Guangxi, 541001, People's Republic of China.,Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, Guilin Medical University, Guilin, Guangxi, 541001, People's Republic of China
| | - Kai Huang
- Laboratory of Hepatobiliary and Pancreatic Surgery, The Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, 541001, People's Republic of China.,China-USA Lipids in Health and Disease Research Center, Guilin Medical University, Guilin, Guangxi, 541001, People's Republic of China.,Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, Guilin Medical University, Guilin, Guangxi, 541001, People's Republic of China
| | - Junfei Jin
- Laboratory of Hepatobiliary and Pancreatic Surgery, The Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, 541001, People's Republic of China. .,China-USA Lipids in Health and Disease Research Center, Guilin Medical University, Guilin, Guangxi, 541001, People's Republic of China. .,Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, Guilin Medical University, Guilin, Guangxi, 541001, People's Republic of China.
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9
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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: 2.5] [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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Sankarasubramanian J, Vishnu US, Gunasekaran P, Rajendhran J. Development and evaluation of a core genome multilocus sequence typing (cgMLST) scheme for Brucella spp. INFECTION GENETICS AND EVOLUTION 2019; 67:38-43. [DOI: 10.1016/j.meegid.2018.10.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 09/29/2018] [Accepted: 10/27/2018] [Indexed: 10/28/2022]
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11
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Ghattargi VC, Gaikwad MA, Meti BS, Nimonkar YS, Dixit K, Prakash O, Shouche YS, Pawar SP, Dhotre DP. Comparative genome analysis reveals key genetic factors associated with probiotic property in Enterococcus faecium strains. BMC Genomics 2018; 19:652. [PMID: 30180794 PMCID: PMC6122445 DOI: 10.1186/s12864-018-5043-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 08/27/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Enterococcus faecium though commensal in the human gut, few strains provide a beneficial effect to humans as probiotics while few are responsible for the nosocomial infection. Comparative genomics of E. faecium can decipher the genomic differences responsible for probiotic, pathogenic and non-pathogenic properties. In this study, we compared E. faecium strain 17OM39 with a marketed probiotic, non-pathogenic non-probiotic (NPNP) and pathogenic strains. RESULTS E. faecium 17OM39 was found to be closely related with marketed probiotic strain T110 based on core genome analysis. Strain 17OM39 was devoid of known vancomycin, tetracycline resistance and functional virulence genes. Moreover, E. faecium 17OM39 genome was found to be more stable due to the absence of frequently found transposable elements. Genes imparting beneficial functional properties were observed to be present in marketed probiotic T110 and 17OM39 strains. Genes associated with colonization and survival within gastrointestinal tract was also detected across all the strains. CONCLUSIONS Beyond shared genetic features; this study particularly identified genes that are responsible for imparting probiotic, non-pathogenic and pathogenic features to the strains of E. faecium. Higher genomic stability, absence of known virulence factors and antibiotic resistance genes and close genomic relatedness with marketed probiotics makes E. faecium 17OM39 a potential probiotic candidate. The work presented here demonstrates that comparative genome analyses can be applied to large numbers of genomes, to find potential probiotic candidates.
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Affiliation(s)
- Vikas C. Ghattargi
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune, Maharashtra 411021 India
- Department of Biotechnology, Basaveshwar Engineering College, Bagalkot, Karnataka 587102 India
| | - Meghana A. Gaikwad
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune, Maharashtra 411021 India
| | - Bharati S. Meti
- Department of Biotechnology, Basaveshwar Engineering College, Bagalkot, Karnataka 587102 India
| | - Yogesh S. Nimonkar
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune, Maharashtra 411021 India
| | - Kunal Dixit
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune, Maharashtra 411021 India
| | - Om Prakash
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune, Maharashtra 411021 India
| | - Yogesh S. Shouche
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune, Maharashtra 411021 India
| | - Shrikant P. Pawar
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune, Maharashtra 411021 India
| | - Dhiraj P. Dhotre
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune, Maharashtra 411021 India
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12
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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: 0.9] [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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13
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Sali M, De Maio F, Tarantino M, Garofolo G, Tittarelli M, Sacchini L, Zilli K, Pasquali P, Petrucci P, Marianelli C, Francia M, Sanguinetti M, Adone R. Rapid and safe one-step extraction method for the identification of Brucella strains at genus and species level by MALDI-TOF mass spectrometry. PLoS One 2018; 13:e0197864. [PMID: 29870530 PMCID: PMC5988274 DOI: 10.1371/journal.pone.0197864] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 05/09/2018] [Indexed: 12/21/2022] Open
Abstract
Brucellosis is essentially a disease of domesticated livestock; however, humans can also be infected via the consumption of contaminated meat or dairy products, underlying the need for rapid and accurate identification methods. Procedures for microbiological identification and typing of Brucella spp. are expensive, time-consuming, and must be conducted in biohazard containment facilities to minimize operator risk. The development of a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS)-based assay has reduced the processing time while maintaining performance standards. In this study, to improve the identification accuracy and suitability of the MALDI-TOF-based assay for routine diagnosis, we developed a new protein extraction protocol and generated a custom reference database containing Brucella strains representative of the most widespread species. The reference library was then challenged with blind-coded field samples isolated from infected animals. The results indicated that the database could be used to correctly identify 99.5% and 97% of Brucella strains at the genus and species level, respectively, indicating that the performance of the assay was not affected by the different culture conditions used for microbial isolation. Moreover, the inactivated samples were stored and shipped to reference laboratories with no ill effect on protein stability, thus confirming the reliability of our method for routine diagnosis. Finally, we evaluated the epidemiological value of the protocol by comparing the clustering analysis results of Brucella melitensis strains obtained via multiple locus variable-number tandem repeat analysis or MALDI-TOF MS. The results showed that the MALDI-TOF assay could not decipher the true phylogenetic tree, suggesting that the protein profile did not correspond with the genetic evolution of Brucella.
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Affiliation(s)
- Michela Sali
- Insitute of Microbiology, Fondazione Policlinico A. Gemelli - IRCCS - Università Cattolica del Sacro Cuore, Rome, Italy
- * E-mail:
| | - Flavio De Maio
- Insitute of Microbiology, Fondazione Policlinico A. Gemelli - IRCCS - Università Cattolica del Sacro Cuore, Rome, Italy
| | - Michela Tarantino
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | - Giuliano Garofolo
- National and OIE Reference Laboratory for Brucellosis, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
| | - Manuela Tittarelli
- National and OIE Reference Laboratory for Brucellosis, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
| | - Lorena Sacchini
- National and OIE Reference Laboratory for Brucellosis, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
| | - Katiuscia Zilli
- National and OIE Reference Laboratory for Brucellosis, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
| | - Paolo Pasquali
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | - Paola Petrucci
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | - Cinzia Marianelli
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | - Massimiliano Francia
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | - Maurizio Sanguinetti
- Insitute of Microbiology, Fondazione Policlinico A. Gemelli - IRCCS - Università Cattolica del Sacro Cuore, Rome, Italy
| | - Rosanna Adone
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy
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14
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Sun M, Jing Z, Di D, Yan H, Zhang Z, Xu Q, Zhang X, Wang X, Ni B, Sun X, Yan C, Yang Z, Tian L, Li J, Fan W. Multiple Locus Variable-Number Tandem-Repeat and Single-Nucleotide Polymorphism-Based Brucella Typing Reveals Multiple Lineages in Brucella melitensis Currently Endemic in China. Front Vet Sci 2017; 4:215. [PMID: 29312964 PMCID: PMC5735110 DOI: 10.3389/fvets.2017.00215] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 11/29/2017] [Indexed: 01/20/2023] Open
Abstract
Brucellosis is a worldwide zoonotic disease caused by Brucella spp. In China, brucellosis is recognized as a reemerging disease mainly caused by Brucella melitensis specie. To better understand the currently endemic B. melitensis strains in China, three Brucella genotyping methods were applied to 110 B. melitensis strains obtained in past several years. By MLVA genotyping, five MLVA-8 genotypes were identified, among which genotypes 42 (1-5-3-13-2-2-3-2) was recognized as the predominant genotype, while genotype 63 (1-5-3-13-2-3-3-2) and a novel genotype of 1-5-3-13-2-4-3-2 were second frequently observed. MLVA-16 discerned a total of 57 MLVA-16 genotypes among these Brucella strains, with 41 genotypes being firstly detected and the other 16 genotypes being previously reported. By BruMLSA21 typing, six sequence types (STs) were identified, among them ST8 is the most frequently seen in China while the other five STs were firstly detected and designated as ST137, ST138, ST139, ST140, and ST141 by international multilocus sequence typing database. Whole-genome sequence (WGS)-single-nucleotide polymorphism (SNP)-based typing and phylogenetic analysis resolved Chinese B. melitensis strains into five clusters, reflecting the existence of multiple lineages among these Chinese B. melitensis strains. In phylogeny, Chinese lineages are more closely related to strains collected from East Mediterranean and Middle East countries, such as Turkey, Kuwait, and Iraq. In the next few years, MLVA typing will certainly remain an important epidemiological tool for Brucella infection analysis, as it displays a high discriminatory ability and achieves result largely in agreement with WGS-SNP-based typing. However, WGS-SNP-based typing is found to be the most powerful and reliable method in discerning Brucella strains and will be popular used in the future.
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Affiliation(s)
- Mingjun Sun
- Laboratory of Zoonoses, Chinese Animal Health and Epidemiology Center, Qingdao, China
| | - Zhigang Jing
- Laboratory of Zoonoses, Chinese Animal Health and Epidemiology Center, Qingdao, China
| | - Dongdong Di
- Laboratory of Zoonoses, Chinese Animal Health and Epidemiology Center, Qingdao, China
| | - Hao Yan
- Xinjiang Center of Animal Disease Control, Urumqi, China
| | - Zhicheng Zhang
- Laboratory of Exotic Disease, Chinese Animal Health and Epidemiology Center, Qingdao, China
| | - Quangang Xu
- Department of Animal Disease Epidemiological Investigation, Animal Health and Epidemiology Center, Qingdao, China
| | - Xiyue Zhang
- Laboratory of Zoonoses, Chinese Animal Health and Epidemiology Center, Qingdao, China
| | - Xun Wang
- Laboratory of Zoonoses, Chinese Animal Health and Epidemiology Center, Qingdao, China
| | - Bo Ni
- Laboratory of Zoonoses, Chinese Animal Health and Epidemiology Center, Qingdao, China
| | - Xiangxiang Sun
- Laboratory of Zoonoses, Chinese Animal Health and Epidemiology Center, Qingdao, China
| | - Chengxu Yan
- Xinjiang Center of Animal Disease Control, Urumqi, China
| | - Zhen Yang
- Laboratory of Zoonoses, Chinese Animal Health and Epidemiology Center, Qingdao, China
| | - Lili Tian
- Laboratory of Zoonoses, Chinese Animal Health and Epidemiology Center, Qingdao, China
| | - Jinping Li
- Xinjiang Center of Animal Disease Control, Urumqi, China
| | - Weixing Fan
- Laboratory of Zoonoses, Chinese Animal Health and Epidemiology Center, Qingdao, China
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15
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Identification of genetic variants of Brucella spp. through genome-wide association studies. INFECTION GENETICS AND EVOLUTION 2017; 56:92-98. [PMID: 29154929 DOI: 10.1016/j.meegid.2017.11.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 11/08/2017] [Accepted: 11/14/2017] [Indexed: 12/25/2022]
Abstract
Brucellosis is an important zoonotic disease caused by Brucella spp. We present a phylogeny of 552 strains based on genome-wide single nucleotide polymorphisms (SNPs) determined by an alignment-free k-mer approach. A total of 138,029 SNPs were identified from 552 Brucella genomes. Of these, 31,152 and 106,877 were core and non-core SNPs, respectively. Based on pan-genome analysis 11,937 and 972 genes were identified as pan and core genome, respectively. The pan-genome-wide analysis studies (Pan-GWAS) could not identify the group-specific variants in Brucella spp. Therefore, we focused on SNP based genome-wide association studies (SNP-GWAS) to identify the species-specific genetic determinants in Brucella spp. Phylogenetic tree representing eleven recognized Brucella spp. showed 16 major lineages. We identified 143 species-specific SNPs in Brucella abortus that are conserved in 311 B. abortus genomes. Of these, 141 species-specific SNPs were confined in the positively significant SNPs of B. abortus using SNP-GWAS. Since conserved in all the B. abortus genomes studied, these SNPs might have originated very early during the evolution of B. abortus and might be responsible for the evolution of B. abortus with cattle as the preferred host. Similarly, we identified 383 species-specific SNPs conserved in 132 Brucella melitensis genomes. Of these 379 species-specific SNPs were identified as positively associated using GWAS. Interestingly, >98% of the SNPs that are significantly, positively associated with the traits showed 100% sensitivity and 100% specificity. These identified species-specific core-SNPs identified in Brucella genomes could be responsible for the speciation and their respective host adaptation.
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16
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Almeida S, Dorneles EMS, Diniz C, Abreu V, Sousa C, Alves J, Carneiro A, Bagano P, Spier S, Barh D, Lage AP, Figueiredo H, Azevedo V. Quadruplex PCR assay for identification of Corynebacterium pseudotuberculosis differentiating biovar Ovis and Equi. BMC Vet Res 2017; 13:290. [PMID: 28946887 PMCID: PMC5613524 DOI: 10.1186/s12917-017-1210-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 09/14/2017] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Corynebacterium pseudotuberculosis is classified into two biovars, nitrate-negative biovar Ovis which is the etiologic agent of caseous lymphadenitis in small ruminants and nitrate-positive biovar Equi, which causes abscesses and ulcerative lymphangitis in equines. The aim of this study was to develop a quadruplex PCR assay that would allow simultaneous detection and biovar-typing of C. pseudotuberculosis. METHODS In the present study, genomes of C. pseudotuberculosis strains were used to identify the genes involved in the nitrate reduction pathway to improve a species identification three-primer multiplex PCR assay. The nitrate reductase gene (narG) was included in the PCR assay along with the 16S, rpoB and pld genes to enhance the diagnosis of the multiplex PCR at biovar level. RESULTS A novel quadruplex PCR assay for C. pseudotuberculosis species and biovar identification was developed. The results of the quadruplex PCR of 348 strains, 346 previously well-characterized clinical isolates of C. pseudotuberculosis from different hosts (goats, sheep, horse, cattle, buffalo, llamas and humans), the vaccine strain 1002 and the type strain ATCC 19410T, were compared to the results of nitrate reductase identification by biochemical test. The McNemar's Chi-squared test used to compare the two methods used for C. pseudotuberculosis biovar identification showed no significant difference (P = 0.75) [95% CI for odds ratio (0.16-6.14)] between the quadruplex PCR and the nitrate biochemical test. Concordant results were observed for 97.13% (338 / 348) of the tested strains and the kappa value was 0.94 [95% CI (0.90-0.98)]. CONCLUSIONS The ability of the quadruplex assay to discriminate between C. pseudotuberculosis biovar Ovis and Equi strains enhances its usefulness in the clinical microbiology laboratory.
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Affiliation(s)
- Sintia Almeida
- Instituto de Ciências Biológicas, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| | - Elaine M. S. Dorneles
- Escola de Veterinária, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| | - Carlos Diniz
- Instituto de Ciências Biológicas, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
- Departamento de Medicina Veterinária, Federal University of Lavras, Lavras, MG Brazil
| | - Vinícius Abreu
- Centro de Energia Nuclear na Agricultura, University of Sao Paulo, Piracicaba, SP Brazil
| | - Cassiana Sousa
- Instituto de Ciências Biológicas, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| | - Jorianne Alves
- Instituto de Ciências Biológicas, Federal University of Para, Belém, PA Brazil
| | - Adriana Carneiro
- Instituto de Ciências Biológicas, Federal University of Para, Belém, PA Brazil
| | - Priscilla Bagano
- Instituto de Ciências Biológicas, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| | - Sharon Spier
- Department of Medicine and Epidemiology, UC Davis School of Veterinary Medicine, Davis, CA USA
| | - Debmalya Barh
- Instituto de Ciências Biológicas, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, WB India
| | - Andrey P. Lage
- Escola de Veterinária, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| | - Henrique Figueiredo
- Aquacen - National Reference Laboratory for Aquatic Animal Diseases, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| | - Vasco Azevedo
- Instituto de Ciências Biológicas, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
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17
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Ferreira AC, Tenreiro R, de Sá MIC, Dias R. Evolution and genome specialization of Brucella suis biovar 2 Iberian lineages. BMC Genomics 2017; 18:726. [PMID: 28899413 PMCID: PMC5596481 DOI: 10.1186/s12864-017-4113-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 09/04/2017] [Indexed: 01/06/2023] Open
Abstract
Background Swine brucellosis caused by B. suis biovar 2 is an emergent disease in domestic pigs in Europe. The emergence of this pathogen has been linked to the increase of extensive pig farms and the high density of infected wild boars (Sus scrofa). In Portugal and Spain, the majority of strains share specific molecular characteristics, which allowed establishing an Iberian clonal lineage. However, several strains isolated from wild boars in the North-East region of Spain are similar to strains isolated in different Central European countries. Results Comparative analysis of five newly fully sequenced B. suis biovar 2 strains belonging to the main circulating clones in Iberian Peninsula, with publicly available Brucella spp. genomes, revealed that strains from Iberian clonal lineage share 74% similarity with those reference genomes. Besides the 210 kb translocation event present in all biovar 2 strains, an inversion with 944 kb was presented in chromosome I of strains from the Iberian clone. At left and right crossover points, the inversion disrupted a TRAP dicarboxylate transporter, DctM subunit, and an integral membrane protein TerC. The gene dctM is well conserved in Brucella spp. except in strains from the Iberian clonal lineage. Intraspecies comparative analysis also exposed a number of biovar-, haplotype- and strain-specific insertion-deletion (INDELs) events and single nucleotide polymorphisms (SNPs) that could explain differences in virulence and host specificities. Most discriminative mutations were associated to membrane related molecules (29%) and enzymes involved in catabolism processes (20%). Molecular identification of both B. suis biovar 2 clonal lineages could be easily achieved using the target-PCR procedures established in this work for the evaluated INDELs. Conclusion Whole-genome analyses supports that the B. suis biovar 2 Iberian clonal lineage evolved from the Central-European lineage and suggests that the genomic specialization of this pathogen in the Iberian Peninsula is independent of a specific genomic event(s), but instead driven by allopatric speciation, resulting in the establishment of a new ecovar. Electronic supplementary material The online version of this article (10.1186/s12864-017-4113-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ana Cristina Ferreira
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV, IP), Av. da República, Quinta do Marquês, 2780-157, Oeiras, Portugal. .,Universidade de Lisboa, Faculdade de Ciências, Biosystems and Integrative Sciences Institute (BioISI), Edificio TecLabs, Campus da FCUL, Campo Grande, 1749-016, Lisbon, Portugal.
| | - Rogério Tenreiro
- Universidade de Lisboa, Faculdade de Ciências, Biosystems and Integrative Sciences Institute (BioISI), Edificio TecLabs, Campus da FCUL, Campo Grande, 1749-016, Lisbon, Portugal
| | - Maria Inácia Corrêa de Sá
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV, IP), Av. da República, Quinta do Marquês, 2780-157, Oeiras, Portugal
| | - Ricardo Dias
- Universidade de Lisboa, Faculdade de Ciências, Biosystems and Integrative Sciences Institute (BioISI), Edificio TecLabs, Campus da FCUL, Campo Grande, 1749-016, Lisbon, Portugal
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18
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New Scenarios for Brucella suis and Brucella melitensis. CURRENT CLINICAL MICROBIOLOGY REPORTS 2017. [DOI: 10.1007/s40588-017-0053-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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19
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Olsen SC, Tatum FM. Swine brucellosis: current perspectives. VETERINARY MEDICINE-RESEARCH AND REPORTS 2016; 8:1-12. [PMID: 30050849 PMCID: PMC6042558 DOI: 10.2147/vmrr.s91360] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Brucella suis is a significant zoonotic species that is present in domestic livestock and wildlife in many countries worldwide. Transmission from animal reservoirs is the source of human infection as human-to-human transmission is very rare. Although swine brucellosis causes economic losses in domestic livestock, preventing human infection is the primary reason for its emphasis in disease control programs. Although disease prevalence varies worldwide, in areas outside of Europe, swine brucellosis is predominantly caused by B. suis biovars 1 and 3. In Europe, swine are predominantly infected with biovar 2 which is much less pathogenic in humans. In many areas worldwide, feral or wild populations of swine are important reservoir hosts. Like other Brucella spp. in their natural host, B. suis has developed mechanisms to survive in an intracellular environment and evade immune detection. Limitations in sensitivity and specificity of current diagnostics require use at a herd level, rather for individual animals. There is currently no commercial vaccine approved for preventing brucellosis in swine. Although not feasible in all situations, whole-herd depopulation is the most effective regulatory mechanism to control swine brucellosis.
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Affiliation(s)
- S C Olsen
- Infectious Bacterial Diseases of Livestock Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, USA,
| | - F M Tatum
- Infectious Bacterial Diseases of Livestock Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, USA,
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