Tracking the Distribution of <i>Brucella abortus</i> in Egypt Based on Core Genome SNP Analysis and In Silico MLVA-16
Brucellosis, caused by the bacteria of the genus <i>Brucella</i>, is one of the most neglected common zoonotic diseases globally with a public health significance and a high economic loss among the livestock industry worldwide. Since little is known about the distribution of <i>B....
| 發表在: | Microorganisms |
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| Main Authors: | , , , , , , , , , , , , |
| 格式: | Article |
| 語言: | 英语 |
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MDPI AG
2021-09-01
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| 在線閱讀: | https://www.mdpi.com/2076-2607/9/9/1942 |
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| author | Katharina Holzer Mohamed El-Diasty Gamal Wareth Nour H. Abdel-Hamid Mahmoud E. R. Hamdy Shawky A. Moustafa Jörg Linde Felix Bartusch Ashraf E. Sayour Essam M. Elbauomy Mohamed Elhadidy Falk Melzer Wolfgang Beyer |
| author_facet | Katharina Holzer Mohamed El-Diasty Gamal Wareth Nour H. Abdel-Hamid Mahmoud E. R. Hamdy Shawky A. Moustafa Jörg Linde Felix Bartusch Ashraf E. Sayour Essam M. Elbauomy Mohamed Elhadidy Falk Melzer Wolfgang Beyer |
| author_sort | Katharina Holzer |
| collection | DOAJ |
| container_title | Microorganisms |
| description | Brucellosis, caused by the bacteria of the genus <i>Brucella</i>, is one of the most neglected common zoonotic diseases globally with a public health significance and a high economic loss among the livestock industry worldwide. Since little is known about the distribution of <i>B. abortus</i> in Egypt, a total of 46 <i>B. abortus</i> isolates recovered between 2012–2020, plus one animal isolate from 2006, were analyzed by examining the whole core genome single nucleotide polymorphism (cgSNP) in comparison to the in silico multilocus variable number of tandem repeat analysis (MLVA). Both cgSNP analysis and MLVA revealed three clusters and one isolate only was distantly related to the others. One cluster identified a rather widely distributed outbreak strain which is repeatedly occurring for at least 16 years with marginal deviations in cgSNP analysis. The other cluster of isolates represents a rather newly introduced outbreak strain. A separate cluster comprised RB51 vaccine related strains, isolated from aborted material. The comparison with MLVA data sets from public databases reveals one near relative from Argentina to the oldest outbreak strain and a related strain from Spain to a newly introduced outbreak strain in Egypt. The distantly related isolate matches with a strain from Portugal in the MLVA profile. Based on cgSNP analysis the oldest outbreak strain clusters with strains from the UK. Compared to the in silico analysis of MLVA, cgSNP analysis using WGS data provides a much higher resolution of genotypes and, when correlated to the associated epidemiological metadata, cgSNP analysis allows the differentiation of outbreaks by defining different outbreak strains. In this respect, MLVA data are error-prone and can lead to incorrect interpretations of outbreak events. |
| format | Article |
| id | doaj-art-5dcd979e8d6b44b5a7fa613196971b21 |
| institution | Directory of Open Access Journals |
| issn | 2076-2607 |
| language | English |
| publishDate | 2021-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| spelling | doaj-art-5dcd979e8d6b44b5a7fa613196971b212025-08-19T22:36:42ZengMDPI AGMicroorganisms2076-26072021-09-0199194210.3390/microorganisms9091942Tracking the Distribution of <i>Brucella abortus</i> in Egypt Based on Core Genome SNP Analysis and In Silico MLVA-16Katharina Holzer0Mohamed El-Diasty1Gamal Wareth2Nour H. Abdel-Hamid3Mahmoud E. R. Hamdy4Shawky A. Moustafa5Jörg Linde6Felix Bartusch7Ashraf E. Sayour8Essam M. Elbauomy9Mohamed Elhadidy10Falk Melzer11Wolfgang Beyer12Department of Livestock Infectiology and Environmental Hygiene, Institute of Animal Science, University of Hohenheim, Garbenstraße 30, 70599 Stuttgart, GermanyAgricultural Research Center, Animal Health Research Institute, P.O. Box 264-Giza, Cairo 12618, EgyptFaculty of Veterinary Medicine, Benha University, Moshtohor, Toukh 13736, EgyptAgricultural Research Center, Animal Health Research Institute, P.O. Box 264-Giza, Cairo 12618, EgyptAgricultural Research Center, Animal Health Research Institute, P.O. Box 264-Giza, Cairo 12618, EgyptFaculty of Veterinary Medicine, Benha University, Moshtohor, Toukh 13736, EgyptInstitute of Bacterial Infections and Zoonoses, Friedrich-Loeffler Institut, Naumburger Str. 96a, 07743 Jena, GermanyHigh-Performance and Cloud Computing Group, IT Center (ZDV), University of Tuebingen, Waechterstrasse 76, 72074 Tübingen, GermanyAgricultural Research Center, Animal Health Research Institute, P.O. Box 264-Giza, Cairo 12618, EgyptAgricultural Research Center, Animal Health Research Institute, P.O. Box 264-Giza, Cairo 12618, EgyptBiomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza 12578, EgyptInstitute of Bacterial Infections and Zoonoses, Friedrich-Loeffler Institut, Naumburger Str. 96a, 07743 Jena, GermanyDepartment of Livestock Infectiology and Environmental Hygiene, Institute of Animal Science, University of Hohenheim, Garbenstraße 30, 70599 Stuttgart, GermanyBrucellosis, caused by the bacteria of the genus <i>Brucella</i>, is one of the most neglected common zoonotic diseases globally with a public health significance and a high economic loss among the livestock industry worldwide. Since little is known about the distribution of <i>B. abortus</i> in Egypt, a total of 46 <i>B. abortus</i> isolates recovered between 2012–2020, plus one animal isolate from 2006, were analyzed by examining the whole core genome single nucleotide polymorphism (cgSNP) in comparison to the in silico multilocus variable number of tandem repeat analysis (MLVA). Both cgSNP analysis and MLVA revealed three clusters and one isolate only was distantly related to the others. One cluster identified a rather widely distributed outbreak strain which is repeatedly occurring for at least 16 years with marginal deviations in cgSNP analysis. The other cluster of isolates represents a rather newly introduced outbreak strain. A separate cluster comprised RB51 vaccine related strains, isolated from aborted material. The comparison with MLVA data sets from public databases reveals one near relative from Argentina to the oldest outbreak strain and a related strain from Spain to a newly introduced outbreak strain in Egypt. The distantly related isolate matches with a strain from Portugal in the MLVA profile. Based on cgSNP analysis the oldest outbreak strain clusters with strains from the UK. Compared to the in silico analysis of MLVA, cgSNP analysis using WGS data provides a much higher resolution of genotypes and, when correlated to the associated epidemiological metadata, cgSNP analysis allows the differentiation of outbreaks by defining different outbreak strains. In this respect, MLVA data are error-prone and can lead to incorrect interpretations of outbreak events.https://www.mdpi.com/2076-2607/9/9/1942<i>Brucella abortus</i>SNP analysisgenotypingMLVAoutbreak analysis |
| spellingShingle | Katharina Holzer Mohamed El-Diasty Gamal Wareth Nour H. Abdel-Hamid Mahmoud E. R. Hamdy Shawky A. Moustafa Jörg Linde Felix Bartusch Ashraf E. Sayour Essam M. Elbauomy Mohamed Elhadidy Falk Melzer Wolfgang Beyer Tracking the Distribution of <i>Brucella abortus</i> in Egypt Based on Core Genome SNP Analysis and In Silico MLVA-16 <i>Brucella abortus</i> SNP analysis genotyping MLVA outbreak analysis |
| title | Tracking the Distribution of <i>Brucella abortus</i> in Egypt Based on Core Genome SNP Analysis and In Silico MLVA-16 |
| title_full | Tracking the Distribution of <i>Brucella abortus</i> in Egypt Based on Core Genome SNP Analysis and In Silico MLVA-16 |
| title_fullStr | Tracking the Distribution of <i>Brucella abortus</i> in Egypt Based on Core Genome SNP Analysis and In Silico MLVA-16 |
| title_full_unstemmed | Tracking the Distribution of <i>Brucella abortus</i> in Egypt Based on Core Genome SNP Analysis and In Silico MLVA-16 |
| title_short | Tracking the Distribution of <i>Brucella abortus</i> in Egypt Based on Core Genome SNP Analysis and In Silico MLVA-16 |
| title_sort | tracking the distribution of i brucella abortus i in egypt based on core genome snp analysis and in silico mlva 16 |
| topic | <i>Brucella abortus</i> SNP analysis genotyping MLVA outbreak analysis |
| url | https://www.mdpi.com/2076-2607/9/9/1942 |
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