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Linde J, Brangsch H, Hölzer M, Thomas C, Elschner MC, Melzer F, Tomaso H. Comparison of Illumina and Oxford Nanopore Technology for genome analysis of Francisella tularensis, Bacillus anthracis, and Brucella suis. BMC Genomics 2023; 24:258. [PMID: 37173617 PMCID: PMC10182678 DOI: 10.1186/s12864-023-09343-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND Bacterial epidemiology needs to understand the spread and dissemination of strains in a One Health context. This is important for highly pathogenic bacteria such as Bacillus anthracis, Brucella species, and Francisella tularensis. Whole genome sequencing (WGS) has paved the way for genetic marker detection and high-resolution genotyping. While such tasks are established for Illumina short-read sequencing, Oxford Nanopore Technology (ONT) long-read sequencing has yet to be evaluated for such highly pathogenic bacteria with little genomic variations between strains. In this study, three independent sequencing runs were performed using Illumina, ONT flow cell version 9.4.1, and 10.4 for six strains of each of Ba. anthracis, Br. suis and F. tularensis. Data from ONT sequencing alone, Illumina sequencing alone and two hybrid assembly approaches were compared. RESULTS As previously shown, ONT produces ultra-long reads, while Illumina produces short reads with higher sequencing accuracy. Flow cell version 10.4 improved sequencing accuracy over version 9.4.1. The correct (sub-)species were inferred from all tested technologies, individually. Moreover, the sets of genetic markers for virulence, were almost identical for the respective species. The long reads of ONT allowed to assemble not only chromosomes of all species to near closure, but also virulence plasmids of Ba. anthracis. Assemblies based on nanopore data alone, Illumina data alone, and both hybrid assemblies correctly detected canonical (sub-)clades for Ba. anthracis and F. tularensis as well as multilocus sequence types for Br. suis. For F. tularensis, high-resolution genotyping using core-genome MLST (cgMLST) and core-genome Single-Nucleotide-Polymorphism (cgSNP) typing produced highly comparable results between data from Illumina and both ONT flow cell versions. For Ba. anthracis, only data from flow cell version 10.4 produced similar results to Illumina for both high-resolution typing methods. However, for Br. suis, high-resolution genotyping yielded larger differences comparing Illumina data to data from both ONT flow cell versions. CONCLUSIONS In summary, combining data from ONT and Illumina for high-resolution genotyping might be feasible for F. tularensis and Ba. anthracis, but not yet for Br. suis. The ongoing improvement of nanopore technology and subsequent data analysis may facilitate high-resolution genotyping for all bacteria with highly stable genomes in future.
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Affiliation(s)
- Jörg Linde
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany.
| | - Hanka Brangsch
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany
| | - Martin Hölzer
- Genome Competence Center (MF1), Methodology and Research Infrastructure, Robert Koch Institute, Berlin, Germany
| | - Christine Thomas
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Mandy C Elschner
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany
| | - Falk Melzer
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany
| | - Herbert Tomaso
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany
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2
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Kneipp CC, Rose AM, Robson J, Malik R, Deutscher AT, Wiethoelter AK, Mor SM. Brucella suis in three dogs: presentation, diagnosis and clinical management. Aust Vet J 2023; 101:133-141. [PMID: 36655500 DOI: 10.1111/avj.13227] [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: 09/03/2022] [Revised: 12/01/2022] [Accepted: 12/23/2022] [Indexed: 01/20/2023]
Abstract
Brucella suis is an emerging, zoonotic disease predominantly affecting dogs and humans that engage in feral pig hunting in Australia and other countries. Although B. suis infection in dogs shares some clinical similarities to the host-adapted species (B. canis), B. suis remains an incompletely understood pathogen in dogs with limited published data on its pathogenesis and clinical features. This case series describes the presentations, diagnosis, and clinical management of B. suis infection in three dogs: (1) a bitch with dystocia, abortion and mastitis; (2) an entire male dog with septic arthritis and presumptive osteomyelitis; and (3) a castrated male dog with lymphadenitis. Unique features of these cases are reported including the first documented detection of B. suis from milk and isolation from lymph nodes of canine patients, as well as the follow-up of pups born to a B. suis-infected bitch. Consistent with previous reports, all three dogs showed a favourable clinical response to combination antibiotic therapy with rifampicin and doxycycline. Individually tailored drug regimens were required based on the clinical presentation and other factors, including owner expectations and compliance with therapy as well as a zoonotic risk assessment (generally considered low, except around time of whelping). The authors include their recommendations for the clinical management of dogs that are at-risk or seropositive for B. suis with or without clinical signs or laboratory-confirmed infection.
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Affiliation(s)
- C C Kneipp
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - A M Rose
- School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia
| | - J Robson
- Department of Microbiology and Molecular Pathology, Sullivan Nicolaides Pathology, Brisbane, Queensland, Australia
| | - R Malik
- Centre for Veterinary Education, University of Sydney, Sydney, New South Wales, Australia.,School of Animal and Veterinary Sciences, Albert Pugsley Pl, Charles Sturt University, New South Wales, Australia
| | - A T Deutscher
- Elizabeth MacArthur Agricultural Institute, NSW Department Primary Industries, Menangle, New South Wales, Australia
| | - A K Wiethoelter
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - S M Mor
- Institute of Infection, Veterinary and Ecological Sciences, The University of Liverpool, Liverpool, UK
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3
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Establishment of loop-mediated isothermal amplification for Brucella detection using a warmer pad as a heating source. Biotechniques 2022; 73:142-150. [PMID: 35997071 DOI: 10.2144/btn-2021-0043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The study sought to establish a sensitive and specific on-site loop-mediated isothermal amplification (LAMP) for Brucella heated using a warmer pad. LAMP primers specific to the conserved BvrR gene were designed, and the LAMP reaction was optimized. The heating characteristics of the warmer pad were investigated. The detection validity (specificity, sensitivity) of clinical samples by warmer-pad LAMP (WP-LAMP) was compared with that of qPCR. The WP-LAMP method displayed high specificity and sensitivity for five Brucella gene copies. The detection of 104 clinical samples was 97.1% concordant with quantitative polymerase chain reaction. The results showed the success of the WP-LAMP for on-site detection. The method requires no special equipment and is conducive to the prevention and control of brucellosis.
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4
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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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5
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van Tulden P, Gonzales JL, Kroese M, Engelsma M, de Zwart F, Szot D, Bisselink Y, van Setten M, Koene M, Willemsen P, Roest HJ, van der Giessen J. Monitoring results of wild boar ( Sus scrofa) in The Netherlands: analyses of serological results and the first identification of Brucella suis biovar 2. Infect Ecol Epidemiol 2020; 10:1794668. [PMID: 33224447 PMCID: PMC7595143 DOI: 10.1080/20008686.2020.1794668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
In Europe, wild boar populations pose an increasing risk for livestock and humans due to the transmission of animal and zoonotic infectious diseases, such as African swine fever and brucellosis. Brucella suis is widespread among wild boar in many European countries. In The Netherlands the prevalence of B. suis among wild boar has not been investigated so far, despite the high number of pig farms and the growing wild boar population. The Netherlands has a Brucella-free status for the livestock species. The objective of this study is to investigate the presence and distribution of B. suis in wild boars in The Netherlands and to assess the value of the different laboratory tests available for testing wild boars. A total of 2057 sera and 180 tonsils of wild boar were collected between 2010 and 2015. The sera were tested for Brucella antibodies and the tonsils were tested for Brucella spp. B. suis biovar 2 was detected by MLVA/MLST and culture in wild boar from the province of Limburg, while seropositive wild boar were obtained from the provinces of Limburg, Noord Brabant and Gelderland suggesting the northwards spread of B. suis biovar 2. In this paper, we describe the first isolation of B. suis biovar 2 in wild boar in The Netherlands.
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Affiliation(s)
- Peter van Tulden
- Wageningen Bioveterinary Research (WBVR), Lelystad, The Netherlands
| | - Jose L Gonzales
- Wageningen Bioveterinary Research (WBVR), Lelystad, The Netherlands
| | - Michiel Kroese
- Wageningen Bioveterinary Research (WBVR), Lelystad, The Netherlands
| | - Marc Engelsma
- Wageningen Bioveterinary Research (WBVR), Lelystad, The Netherlands
| | - Frido de Zwart
- Wageningen Bioveterinary Research (WBVR), Lelystad, The Netherlands
| | - Dorota Szot
- Wageningen Bioveterinary Research (WBVR), Lelystad, The Netherlands
| | - Yvette Bisselink
- Wageningen Bioveterinary Research (WBVR), Lelystad, The Netherlands
| | - Marga van Setten
- Wageningen Bioveterinary Research (WBVR), Lelystad, The Netherlands
| | - Miriam Koene
- Wageningen Bioveterinary Research (WBVR), Lelystad, The Netherlands
| | - Peter Willemsen
- Wageningen Bioveterinary Research (WBVR), Lelystad, The Netherlands
| | | | - Joke van der Giessen
- Wageningen Bioveterinary Research (WBVR), Lelystad, The Netherlands.,National Institute of Public Health and the Environment (RIVM), Bilthoven, The Netherlands
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6
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Khan AU, Sayour AE, Melzer F, El-Soally SAGE, Elschner MC, Shell WS, Moawad AA, Mohamed SA, Hendam A, Roesler U, Neubauer H, El-Adawy H. Seroprevalence and Molecular Identification of Brucella spp. in Camels in Egypt. Microorganisms 2020; 8:microorganisms8071035. [PMID: 32668648 PMCID: PMC7409340 DOI: 10.3390/microorganisms8071035] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 12/21/2022] Open
Abstract
Brucellosis is one of the most important worldwide zoonoses of many countries including Egypt. Camel brucellosis has not gained much attention in Egypt yet. This study is focused on the three governorates with the highest camel populations and the largest camel markets in the country to determine the disease seroprevalence and identify the Brucella species in local camel holdings. In total, 381 serum samples were collected from male and female camels from Giza, Aswan, and Al-Bahr Al-Ahmar (the Red Sea) governorates. Samples were serologically examined using the Rose-Bengal plate test (RBPT), indirect ELISA (i-ELISA), competitive ELISA (c-ELISA) and complement fixation test (CFT). Brucella antibodies were detected in 59 (15.5%), 87 (22.8%), 77 (20.2%) and 118 (31.0%) of sera by RBPT, i-ELISA, c-ELISA and CFT, respectively. Using real-time PCR, Brucella DNA was amplified in 32 (8.4%) seropositive samples including Brucella abortus (25/32), Brucella suis (5/32) and Brucella melitensis (2/32), defining a complex epidemiological status. To the best of our knowledge, this is the first study reporting Brucella suis DNA in camel serum. The risk-associated factors including age, sex, breed and geographical distribution were statistically analyzed, showing non-significant association with seroprevalence. The results of this study will raise awareness for camel brucellosis and help develop effective control strategies.
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Affiliation(s)
- Aman Ullah Khan
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, 07743 Jena, Germany; (A.U.K.); (F.M.); (M.C.E.); (A.A.M.); (H.N.)
- Institut for Animal Hygiene and Environmental Health, Free University of Berlin, 14163 Berlin, Germany;
- Department of Pathobiology, College of Veterinary and Animal Sciences, Jhang 35200, Pakistan
| | - Ashraf E. Sayour
- Department of Brucellosis, Animal Health Research Institute, Agricultural Research Center, Dokki 12618, Giza, Egypt;
| | - Falk Melzer
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, 07743 Jena, Germany; (A.U.K.); (F.M.); (M.C.E.); (A.A.M.); (H.N.)
| | | | - Mandy C. Elschner
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, 07743 Jena, Germany; (A.U.K.); (F.M.); (M.C.E.); (A.A.M.); (H.N.)
| | - Waleed S. Shell
- Central Laboratory for Evaluation of Veterinary Biologics, Agricultural Research Center, Abbasaia 11517, Cairo, Egypt;
| | - Amira A. Moawad
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, 07743 Jena, Germany; (A.U.K.); (F.M.); (M.C.E.); (A.A.M.); (H.N.)
- Provincial Laboratory, Institute of Animal Health Research, Agricultural Research Center, Mansoura 35516, Egypt
| | - Shereen Aziz Mohamed
- Veterinary Serum and Vaccine Research Institute, Agricultural Research Center, Abbasaia 11517, Cairo, Egypt;
| | - Ashraf Hendam
- Climate Change Information Center, Renewable Energy and Expert Systems (CCICREES), Agricultural Research Center, 9 Algamaa Street, Giza 12619, Egypt;
| | - Uwe Roesler
- Institut for Animal Hygiene and Environmental Health, Free University of Berlin, 14163 Berlin, Germany;
| | - Heinrich Neubauer
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, 07743 Jena, Germany; (A.U.K.); (F.M.); (M.C.E.); (A.A.M.); (H.N.)
| | - Hosny El-Adawy
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, 07743 Jena, Germany; (A.U.K.); (F.M.); (M.C.E.); (A.A.M.); (H.N.)
- Faculty of Veterinary Medicine, Kafrelsheikh University, Kafr El-Sheikh 33516, Egypt
- Correspondence:
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7
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Sun M, Liu M, Zhang X, Zhang G, Zhu L, Ding J, Zhang Z, Sun S, Sun S, Shao W, Zhang P, Zhang J, Sun X, Fan X, Wei R. First identification of a Brucella abortus biovar 4 strain from yak in Tibet, China. Vet Microbiol 2020; 247:108751. [PMID: 32768205 DOI: 10.1016/j.vetmic.2020.108751] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 05/29/2020] [Accepted: 06/09/2020] [Indexed: 10/24/2022]
Abstract
Brucellosis is one of the major zoonotic diseases in the world. In China, understanding on its causative agent Brucella is still limited. Recently, we isolated a Brucella strain XZ19-1 from yak in Lhasa, Tibet. Phenotypical characterization proved that it belongs to B. abortus biovar 4, a biotype that has never been reported in China. MLVA-16 genotyping revealed a novel profile (4-5-3-12-2-2-3-3-8-32-8-5-4-3-3-3) in this strain, while MLST sequence typing demonstrated that it belongs to ST 71. Furthermore, the whole genome of XZ19-1 strain was sequenced. Subsequent phylogenetic analysis demonstrated that XZ19-1was genetically more closely related to B. abortus strains originated from European countries rather than to those collected from China previously. Isolation and identification of XZ19-1 strain may thus indicate a unique Brucella lineage existing in Qing-Tibet plateau. These findings will help to improve the diagnosis and epidemiological studies of brucellosis in animals and human in this part of China.
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Affiliation(s)
- Mingjun Sun
- Laboratory of Zoonoses, National Animal Brucellosis Specialized Laboratory, China Animal Health and Epidemiology Center, Qingdao, 266032, China
| | - Mengda Liu
- Laboratory of Zoonoses, National Animal Brucellosis Specialized Laboratory, China Animal Health and Epidemiology Center, Qingdao, 266032, China
| | - Xiyue Zhang
- Laboratory of Zoonoses, National Animal Brucellosis Specialized Laboratory, China Animal Health and Epidemiology Center, Qingdao, 266032, China
| | - Ge Zhang
- National/OIE Animal Brucellosis Reference Laboratory, China Institute of Veterinary Drug Control, Beijing, 100081, China
| | - Liangquan Zhu
- National/OIE Animal Brucellosis Reference Laboratory, China Institute of Veterinary Drug Control, Beijing, 100081, China
| | - Jiabo Ding
- National/OIE Animal Brucellosis Reference Laboratory, China Institute of Veterinary Drug Control, Beijing, 100081, China
| | - Zhicheng Zhang
- Laboratory of Zoonoses, National Animal Brucellosis Specialized Laboratory, China Animal Health and Epidemiology Center, Qingdao, 266032, China
| | - Shixiong Sun
- Laboratory of Zoonoses, National Animal Brucellosis Specialized Laboratory, China Animal Health and Epidemiology Center, Qingdao, 266032, China
| | - Shufang Sun
- Laboratory of Zoonoses, National Animal Brucellosis Specialized Laboratory, China Animal Health and Epidemiology Center, Qingdao, 266032, China
| | - Weixing Shao
- Laboratory of Zoonoses, National Animal Brucellosis Specialized Laboratory, China Animal Health and Epidemiology Center, Qingdao, 266032, China
| | - Peipei Zhang
- Laboratory of Zoonoses, National Animal Brucellosis Specialized Laboratory, China Animal Health and Epidemiology Center, Qingdao, 266032, China
| | - Jiandong Zhang
- Laboratory of Zoonoses, National Animal Brucellosis Specialized Laboratory, China Animal Health and Epidemiology Center, Qingdao, 266032, China
| | - Xiangxiang Sun
- Laboratory of Zoonoses, National Animal Brucellosis Specialized Laboratory, China Animal Health and Epidemiology Center, Qingdao, 266032, China.
| | - Xuezheng Fan
- National/OIE Animal Brucellosis Reference Laboratory, China Institute of Veterinary Drug Control, Beijing, 100081, China.
| | - Rong Wei
- Laboratory of Zoonoses, National Animal Brucellosis Specialized Laboratory, China Animal Health and Epidemiology Center, Qingdao, 266032, China.
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Khan AU, Melzer F, El-Soally SAGE, Elschner MC, Mohamed SA, Sayed Ahmed MA, Roesler U, Neubauer H, El-Adawy H. Serological and Molecular Identification of Brucella spp. in Pigs from Cairo and Giza Governorates, Egypt. Pathogens 2019; 8:pathogens8040248. [PMID: 31756893 PMCID: PMC6963660 DOI: 10.3390/pathogens8040248] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 11/14/2019] [Accepted: 11/16/2019] [Indexed: 12/03/2022] Open
Abstract
Brucellosis is considered as endemic disease of animals and humans since thousands of years in Egypt. However, brucellosis in pigs has never been reported in Egypt. Thus, serological and molecular assays were applied to detect anti-Brucella antibodies and DNA in serum samples collected from pigs. In total 331 blood samples collected from male and female pigs at slaughterhouses of Cairo and Giza governorates were investigated using Brucella c- and i-ELISA and Brucella real-time PCR. Anti-Brucella antibodies were detected in 16 (4.83%) and 36 (10.8%) sera by i-ELISA and c-ELISA, respectively. Brucella DNA was detected in 10 (3.02%) seropositive samples and identified as Brucella melitensis (7/10) and Brucella suis (3/10). A higher prevelance was found in boars. This is the first study investigating pig brucellosis in Egypt. The results of this study will raise awareness for brucellosis in these farm animals and will help to develop effective control strategies.
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Affiliation(s)
- Aman Ullah Khan
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, 07743 Jena, Germany; (A.U.K.); (F.M.); (M.C.E.); (H.N.)
- Institute for Animal Hygiene and Environmental Health, Free University of Berlin, 14163 Berlin, Germany;
- Department of Pathobiology, College of Veterinary and Animal Sciences (Sub-Campus UVAS-Lahore), Jhang 35200, Pakistan
| | - Falk Melzer
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, 07743 Jena, Germany; (A.U.K.); (F.M.); (M.C.E.); (H.N.)
| | | | - Mandy C. Elschner
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, 07743 Jena, Germany; (A.U.K.); (F.M.); (M.C.E.); (H.N.)
| | | | - Mohamed Abdelmonem Sayed Ahmed
- Veterinary Service Department, Armed Forces Logistics Authority, Egyptian Armed Forces, 11765 Nasr City, Egypt (M.A.S.A.)
| | - Uwe Roesler
- Institute for Animal Hygiene and Environmental Health, Free University of Berlin, 14163 Berlin, Germany;
| | - Heinrich Neubauer
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, 07743 Jena, Germany; (A.U.K.); (F.M.); (M.C.E.); (H.N.)
| | - Hosny El-Adawy
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, 07743 Jena, Germany; (A.U.K.); (F.M.); (M.C.E.); (H.N.)
- Faculty of Veterinary Medicine, Kafrelsheikh University, 33516 Kafr El-Sheikh, Egypt
- Correspondence:
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Feau N, Beauseigle S, Bergeron MJ, Bilodeau GJ, Birol I, Cervantes-Arango S, Dhillon B, Dale AL, Herath P, Jones SJ, Lamarche J, Ojeda DI, Sakalidis ML, Taylor G, Tsui CK, Uzunovic A, Yueh H, Tanguay P, Hamelin RC. Genome-Enhanced Detection and Identification (GEDI) of plant pathogens. PeerJ 2018; 6:e4392. [PMID: 29492338 PMCID: PMC5825881 DOI: 10.7717/peerj.4392] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 01/29/2018] [Indexed: 12/17/2022] Open
Abstract
Plant diseases caused by fungi and Oomycetes represent worldwide threats to crops and forest ecosystems. Effective prevention and appropriate management of emerging diseases rely on rapid detection and identification of the causal pathogens. The increase in genomic resources makes it possible to generate novel genome-enhanced DNA detection assays that can exploit whole genomes to discover candidate genes for pathogen detection. A pipeline was developed to identify genome regions that discriminate taxa or groups of taxa and can be converted into PCR assays. The modular pipeline is comprised of four components: (1) selection and genome sequencing of phylogenetically related taxa, (2) identification of clusters of orthologous genes, (3) elimination of false positives by filtering, and (4) assay design. This pipeline was applied to some of the most important plant pathogens across three broad taxonomic groups: Phytophthoras (Stramenopiles, Oomycota), Dothideomycetes (Fungi, Ascomycota) and Pucciniales (Fungi, Basidiomycota). Comparison of 73 fungal and Oomycete genomes led the discovery of 5,939 gene clusters that were unique to the targeted taxa and an additional 535 that were common at higher taxonomic levels. Approximately 28% of the 299 tested were converted into qPCR assays that met our set of specificity criteria. This work demonstrates that a genome-wide approach can efficiently identify multiple taxon-specific genome regions that can be converted into highly specific PCR assays. The possibility to easily obtain multiple alternative regions to design highly specific qPCR assays should be of great help in tackling challenging cases for which higher taxon-resolution is needed.
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Affiliation(s)
- Nicolas Feau
- Department of Forest and Conservation Sciences, Forest Sciences Centre, University of British Columbia, Vancouver, BC, Canada
| | | | | | | | - Inanc Birol
- BC Cancer agency, Genome Sciences Centre, Vancouver, BC, Canada
| | - Sandra Cervantes-Arango
- Department of Forest and Conservation Sciences, Forest Sciences Centre, University of British Columbia, Vancouver, BC, Canada
| | - Braham Dhillon
- Department of Plant Pathology, University of Arkansas at Fayetteville, Fayetteville, AR, United States of America
| | - Angela L. Dale
- Department of Forest and Conservation Sciences, Forest Sciences Centre, University of British Columbia, Vancouver, BC, Canada
- FPInnovations, Vancouver, BC, Canada
| | - Padmini Herath
- Department of Forest and Conservation Sciences, Forest Sciences Centre, University of British Columbia, Vancouver, BC, Canada
| | - Steven J.M. Jones
- BC Cancer agency, Genome Sciences Centre, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Josyanne Lamarche
- Canadian Forest Service, Natural Resources Canada, Quebec city, Quebec, Canada
| | - Dario I. Ojeda
- Department of Biology Unit of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Monique L. Sakalidis
- Department of Plant, Soil & Microbial Sciences and Department of Forestry, Michigan State University, East Lansing, MI, United States of America
| | - Greg Taylor
- BC Cancer agency, Genome Sciences Centre, Vancouver, BC, Canada
| | - Clement K.M. Tsui
- Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | | | - Hesther Yueh
- Department of Forest and Conservation Sciences, Forest Sciences Centre, University of British Columbia, Vancouver, BC, Canada
| | - Philippe Tanguay
- Canadian Forest Service, Natural Resources Canada, Quebec city, Quebec, Canada
| | - Richard C. Hamelin
- Department of Forest and Conservation Sciences, Forest Sciences Centre, University of British Columbia, Vancouver, BC, Canada
- Foresterie et géomatique, Institut de Biologie Intégrative des Systèmes, Laval University, Quebec city, Quebec, Canada
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Highly Sensitive Bacteriophage-Based Detection of Brucella abortus in Mixed Culture and Spiked Blood. Viruses 2017; 9:v9060144. [PMID: 28604602 PMCID: PMC5490821 DOI: 10.3390/v9060144] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 05/25/2017] [Accepted: 06/06/2017] [Indexed: 01/18/2023] Open
Abstract
For decades, bacteriophages (phages) have been used for Brucella species identification in the diagnosis and epidemiology of brucellosis. Traditional Brucella phage typing is a multi-day procedure including the isolation of a pure culture, a step that can take up to three weeks. In this study, we focused on the use of brucellaphages for sensitive detection of the pathogen in clinical and other complex samples, and developed an indirect method of Brucella detection using real-time quantitative PCR monitoring of brucellaphage DNA amplification via replication on live Brucella cells. This assay allowed the detection of single bacteria (down to 1 colony-forming unit per milliliter) within 72 h without DNA extraction and purification steps. The technique was equally efficient with Brucella abortus pure culture and with mixed cultures of B. abortus and α-proteobacterial near neighbors that can be misidentified as Brucella spp., Ochrobactrum anthropi and Afipia felis. The addition of a simple short sample preparation step enabled the indirect phage-based detection of B. abortus in spiked blood, with the same high sensitivity. This indirect phage-based detection assay enables the rapid and sensitive detection of live B. abortus in mixed cultures and in blood samples, and can potentially be applied for detection in other clinical samples and other complex sample types.
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Grunow R, Jacob D, Klee S, Schlembach D, Jackowski-Dohrmann S, Loenning-Baucke V, Eberspächer B, Swidsinski S. Brucellosis in a refugee who migrated from Syria to Germany and lessons learnt, 2016. ACTA ACUST UNITED AC 2017; 21:30311. [PMID: 27525454 PMCID: PMC4998511 DOI: 10.2807/1560-7917.es.2016.21.31.30311] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 08/03/2016] [Indexed: 11/20/2022]
Abstract
A teenage woman migrating from Syria arrived in May 2015 in Germany. She gave birth to a healthy child in early 2016, but became febrile shortly after delivery. Blood cultures revealed Brucella melitensis. In retrospect, she reported contact with sheep in Syria and recurrent pain in the hip joints over about five months before diagnosis of brucellosis. We discuss consequences for adequate treatment of mother and child as well as for clinical and laboratory management.
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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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13
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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: 26] [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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Rahi A, Sattarahmady N, Heli H. An ultrasensitive electrochemical genosensor for Brucella based on palladium nanoparticles. Anal Biochem 2016; 510:11-17. [DOI: 10.1016/j.ab.2016.07.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Revised: 07/06/2016] [Accepted: 07/11/2016] [Indexed: 01/10/2023]
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Tiwari AP, Rohiwal SS, Suryavanshi MV, Ghosh SJ, Pawar SH. Detection of the genomic DNA of pathogenic α-proteobacterium Ochrobactrum anthropi via magnetic DNA enrichment using pH responsive BSA@Fe3O4 nanoparticles prior to in-situ PCR and electrophoretic separation. Mikrochim Acta 2015. [DOI: 10.1007/s00604-015-1710-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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