Sequencing-Based Genotyping of Pakistani <i>Burkholderia mallei</i> Strains: A Useful Way for Investigating Glanders Outbreaks
<i>Burkholderia</i> (<i>B.</i>) <i>mallei</i> is a host-adapted equine pathogen that causes glanders, a re-emerging zoonotic disease, which is endemic in Pakistan and other developing countries and seriously impacts the global equine movement. Due to globalization...
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| Format: | Article |
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MDPI AG
2022-05-01
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| Series: | Pathogens |
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| Online Access: | https://www.mdpi.com/2076-0817/11/6/614 |
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| author | Hanka Brangsch Muhammad Saqib Awais ur Rehman Sial Falk Melzer Jörg Linde Mandy Carolina Elschner |
| author_facet | Hanka Brangsch Muhammad Saqib Awais ur Rehman Sial Falk Melzer Jörg Linde Mandy Carolina Elschner |
| author_sort | Hanka Brangsch |
| collection | DOAJ |
| description | <i>Burkholderia</i> (<i>B.</i>) <i>mallei</i> is a host-adapted equine pathogen that causes glanders, a re-emerging zoonotic disease, which is endemic in Pakistan and other developing countries and seriously impacts the global equine movement. Due to globalization, the geographical restriction of diseases vanishes and the lack of awareness of and experience with eradicated diseases in industrialized countries also promotes the re-introduction of infections in these regions. Owing to the high equine population, the Pakistani province Punjab is a potential hotspot where several glanders outbreaks have been seen over last two decades. For determining the genomic diversity of <i>B. mallei</i> in this and other equine-populated prefectures, the genomes of 19 <i>B. mallei</i> strains isolated between 1999 and 2020 in different locations were sequenced and their genotypes were determined. Particularly, for genetically highly homogenous pathogens like <i>B. mallei</i> genotyping techniques require a high discriminatory power for enabling differentiation on the strain level. Thus, core-genome single nucleotide polymorphism (cgSNP) analysis was applied for distinguishing the highly similar strains. Furthermore, a whole-genome sequence-based core genome multi locus sequence typing (cgMLST) scheme, specific to <i>B. mallei</i>, was developed and additionally applied to the data. It was found that <i>B. mallei</i> genotypes in Pakistan persisted over time and space and genotype clusters preferred connection with a time point rather than the place of isolation, probably due to frequent equine movement, which promotes the spread of glanders. The cgMLST approach proved to work in accord with SNP typing and may help to investigate future glanders outbreaks. |
| first_indexed | 2024-03-09T22:48:23Z |
| format | Article |
| id | doaj.art-5c7b89819f374f74b7ae1df43610737a |
| institution | Directory Open Access Journal |
| issn | 2076-0817 |
| language | English |
| last_indexed | 2024-03-09T22:48:23Z |
| publishDate | 2022-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Pathogens |
| spelling | doaj.art-5c7b89819f374f74b7ae1df43610737a2023-11-23T18:24:05ZengMDPI AGPathogens2076-08172022-05-0111661410.3390/pathogens11060614Sequencing-Based Genotyping of Pakistani <i>Burkholderia mallei</i> Strains: A Useful Way for Investigating Glanders OutbreaksHanka Brangsch0Muhammad Saqib1Awais ur Rehman Sial2Falk Melzer3Jörg Linde4Mandy Carolina Elschner5Institute for Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Naumburger Str. 96a, 07743 Jena, Thuringia, GermanyVeterinary Preventive Medicine and Public Health Laboratory, Department of Clinical Medicine and Surgery, University of Agriculture, Faisalabad 38000, PakistanDepartment of Clinical Studies, Faculty of Veterinary and Animal Science, Pir Mehr Ali Shah, Arid Agriculture University Rawalpindi, Rawalpindi 46000, PakistanInstitute for Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Naumburger Str. 96a, 07743 Jena, Thuringia, GermanyInstitute for Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Naumburger Str. 96a, 07743 Jena, Thuringia, GermanyInstitute for Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Naumburger Str. 96a, 07743 Jena, Thuringia, Germany<i>Burkholderia</i> (<i>B.</i>) <i>mallei</i> is a host-adapted equine pathogen that causes glanders, a re-emerging zoonotic disease, which is endemic in Pakistan and other developing countries and seriously impacts the global equine movement. Due to globalization, the geographical restriction of diseases vanishes and the lack of awareness of and experience with eradicated diseases in industrialized countries also promotes the re-introduction of infections in these regions. Owing to the high equine population, the Pakistani province Punjab is a potential hotspot where several glanders outbreaks have been seen over last two decades. For determining the genomic diversity of <i>B. mallei</i> in this and other equine-populated prefectures, the genomes of 19 <i>B. mallei</i> strains isolated between 1999 and 2020 in different locations were sequenced and their genotypes were determined. Particularly, for genetically highly homogenous pathogens like <i>B. mallei</i> genotyping techniques require a high discriminatory power for enabling differentiation on the strain level. Thus, core-genome single nucleotide polymorphism (cgSNP) analysis was applied for distinguishing the highly similar strains. Furthermore, a whole-genome sequence-based core genome multi locus sequence typing (cgMLST) scheme, specific to <i>B. mallei</i>, was developed and additionally applied to the data. It was found that <i>B. mallei</i> genotypes in Pakistan persisted over time and space and genotype clusters preferred connection with a time point rather than the place of isolation, probably due to frequent equine movement, which promotes the spread of glanders. The cgMLST approach proved to work in accord with SNP typing and may help to investigate future glanders outbreaks.https://www.mdpi.com/2076-0817/11/6/614glanders<i>Burkholderia mallei</i>SNP typingcgMLST schemegenotypingPakistan |
| spellingShingle | Hanka Brangsch Muhammad Saqib Awais ur Rehman Sial Falk Melzer Jörg Linde Mandy Carolina Elschner Sequencing-Based Genotyping of Pakistani <i>Burkholderia mallei</i> Strains: A Useful Way for Investigating Glanders Outbreaks Pathogens glanders <i>Burkholderia mallei</i> SNP typing cgMLST scheme genotyping Pakistan |
| title | Sequencing-Based Genotyping of Pakistani <i>Burkholderia mallei</i> Strains: A Useful Way for Investigating Glanders Outbreaks |
| title_full | Sequencing-Based Genotyping of Pakistani <i>Burkholderia mallei</i> Strains: A Useful Way for Investigating Glanders Outbreaks |
| title_fullStr | Sequencing-Based Genotyping of Pakistani <i>Burkholderia mallei</i> Strains: A Useful Way for Investigating Glanders Outbreaks |
| title_full_unstemmed | Sequencing-Based Genotyping of Pakistani <i>Burkholderia mallei</i> Strains: A Useful Way for Investigating Glanders Outbreaks |
| title_short | Sequencing-Based Genotyping of Pakistani <i>Burkholderia mallei</i> Strains: A Useful Way for Investigating Glanders Outbreaks |
| title_sort | sequencing based genotyping of pakistani i burkholderia mallei i strains a useful way for investigating glanders outbreaks |
| topic | glanders <i>Burkholderia mallei</i> SNP typing cgMLST scheme genotyping Pakistan |
| url | https://www.mdpi.com/2076-0817/11/6/614 |
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