New genetic markers for <i>Burkholderia pseudomallei</i> strains typing
Burkholderia pseudomallei is the causative agent of melioidosis, a serious infectious disease in humans and animals that may be asymptomatic long-term and quickly develop to pneumonia and septicemia in immunocompromised state and due to predisposing factors. Melioidosis is endemic in countries with...
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| Format: | Article |
| Language: | Russian |
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Sankt-Peterburg : NIIÈM imeni Pastera
2022-12-01
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| Series: | Инфекция и иммунитет |
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| Online Access: | https://iimmun.ru/iimm/article/viewFile/1965/1497 |
| _version_ | 1797957293033127936 |
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| author | Margarita L. Ledenyova Galina A. Tkachenko Irina B. Zakharova |
| author_facet | Margarita L. Ledenyova Galina A. Tkachenko Irina B. Zakharova |
| author_sort | Margarita L. Ledenyova |
| collection | DOAJ |
| description | Burkholderia pseudomallei is the causative agent of melioidosis, a serious infectious disease in humans and animals that may be asymptomatic long-term and quickly develop to pneumonia and septicemia in immunocompromised state and due to predisposing factors. Melioidosis is endemic in countries with tropical and subtropical climates, where B. pseudomallei is a part of the soil and water microbiota of stagnant water bodies, as well as the plant rhizosphere. The recording of imported melioidosis cases in countries with temperate climate zone, along with the continued threat of using this pathogen as a bioterrorism agent, indicate the relevance of research aimed at developing modern methods for its diagnosing and typing. Current research in the intraspecific differentiation of pathogenic strains of infectious diseases tends to use two or more types of molecular markers. A promising direction for the B. pseudomallei strains genotyping is based on using a combination of VNTR loci, which provides a high discriminating ability of the method of multi-locus variable tandem repeat number analysis (MLVA), and slowly evolving single nucleotide polymorphisms (SNPs). The aim of this work was to identify new VNTR and SNP loci suitable for use as genetic markers in molecular typing of the melioidosis causative agent. 20 strains of B. pseudomallei from the collection of the Volgograd Plague Control Research Institute and whole genome sequences of 85 B. pseudomallei strains from the GenBank NCBI database were analyzed. While typing melioidosis causative agent strains from the GenBank NCBI database for 4 VNTR loci, 74 genotypes were identified, of which 64 were unique (HunterGaston index 0.997). It was found that the high allelic polymorphism of VNTR loci limited a potential to determine the geographical and phylogenetic relationships of B. pseudomallei isolates by using the MLVA-4 scheme, and the identified null alleles increased the risk of homoplasia. In this regard, the MLVA-4 scheme was supplemented with a VNTR marker in the BPSS1974 locus encoding a collagen-like protein as well as with SNP markers in the genes of lipid A biosynthesis lauroyl acyltransferase, RNA polymerase sigma factor RpoH, and glutamine amidotransferase. For amplification of the select loci, primers and probes were designed as part of the developed scheme, which were tested in the typing of B. pseudomallei collection strains. According to the results of a cluster analysis for 105 strains of the melioidosis causative agent, an integrated approach turned out to be optimal, allowing differentiation of strains within SNP groups based on VNTR profiles. The methodological approach developed for B. pseudomallei genetic typing, based on a comprehensive analysis of 4 SNP- and 5 MLVA-markers in our modification, allowed to differentiate strains according to the geographical regions of their origin and establish the clonal origin of isolates upon revealing cases of melioidosis. |
| first_indexed | 2024-04-11T00:02:06Z |
| format | Article |
| id | doaj.art-579692ae0c554f67941ffe5d6961fd67 |
| institution | Directory Open Access Journal |
| issn | 2220-7619 2313-7398 |
| language | Russian |
| last_indexed | 2024-04-11T00:02:06Z |
| publishDate | 2022-12-01 |
| publisher | Sankt-Peterburg : NIIÈM imeni Pastera |
| record_format | Article |
| series | Инфекция и иммунитет |
| spelling | doaj.art-579692ae0c554f67941ffe5d6961fd672023-01-09T16:59:58ZrusSankt-Peterburg : NIIÈM imeni PasteraИнфекция и иммунитет2220-76192313-73982022-12-011261091110210.15789/2220-7619-NGM-19651239New genetic markers for <i>Burkholderia pseudomallei</i> strains typingMargarita L. Ledenyova0https://orcid.org/0000-0001-5923-4774Galina A. Tkachenko1https://orcid.org/0000-0003-0199-3342Irina B. Zakharova2https://orcid.org/0000-0002-7808-7658Volgograd Plague Control Research InstituteVolgograd Plague Control Research InstituteVolgograd Plague Control Research InstituteBurkholderia pseudomallei is the causative agent of melioidosis, a serious infectious disease in humans and animals that may be asymptomatic long-term and quickly develop to pneumonia and septicemia in immunocompromised state and due to predisposing factors. Melioidosis is endemic in countries with tropical and subtropical climates, where B. pseudomallei is a part of the soil and water microbiota of stagnant water bodies, as well as the plant rhizosphere. The recording of imported melioidosis cases in countries with temperate climate zone, along with the continued threat of using this pathogen as a bioterrorism agent, indicate the relevance of research aimed at developing modern methods for its diagnosing and typing. Current research in the intraspecific differentiation of pathogenic strains of infectious diseases tends to use two or more types of molecular markers. A promising direction for the B. pseudomallei strains genotyping is based on using a combination of VNTR loci, which provides a high discriminating ability of the method of multi-locus variable tandem repeat number analysis (MLVA), and slowly evolving single nucleotide polymorphisms (SNPs). The aim of this work was to identify new VNTR and SNP loci suitable for use as genetic markers in molecular typing of the melioidosis causative agent. 20 strains of B. pseudomallei from the collection of the Volgograd Plague Control Research Institute and whole genome sequences of 85 B. pseudomallei strains from the GenBank NCBI database were analyzed. While typing melioidosis causative agent strains from the GenBank NCBI database for 4 VNTR loci, 74 genotypes were identified, of which 64 were unique (HunterGaston index 0.997). It was found that the high allelic polymorphism of VNTR loci limited a potential to determine the geographical and phylogenetic relationships of B. pseudomallei isolates by using the MLVA-4 scheme, and the identified null alleles increased the risk of homoplasia. In this regard, the MLVA-4 scheme was supplemented with a VNTR marker in the BPSS1974 locus encoding a collagen-like protein as well as with SNP markers in the genes of lipid A biosynthesis lauroyl acyltransferase, RNA polymerase sigma factor RpoH, and glutamine amidotransferase. For amplification of the select loci, primers and probes were designed as part of the developed scheme, which were tested in the typing of B. pseudomallei collection strains. According to the results of a cluster analysis for 105 strains of the melioidosis causative agent, an integrated approach turned out to be optimal, allowing differentiation of strains within SNP groups based on VNTR profiles. The methodological approach developed for B. pseudomallei genetic typing, based on a comprehensive analysis of 4 SNP- and 5 MLVA-markers in our modification, allowed to differentiate strains according to the geographical regions of their origin and establish the clonal origin of isolates upon revealing cases of melioidosis.https://iimmun.ru/iimm/article/viewFile/1965/1497burkholderia pseudomalleigenotypingmlvasnpsphylogeographytandem repeats |
| spellingShingle | Margarita L. Ledenyova Galina A. Tkachenko Irina B. Zakharova New genetic markers for <i>Burkholderia pseudomallei</i> strains typing Инфекция и иммунитет burkholderia pseudomallei genotyping mlva snps phylogeography tandem repeats |
| title | New genetic markers for <i>Burkholderia pseudomallei</i> strains typing |
| title_full | New genetic markers for <i>Burkholderia pseudomallei</i> strains typing |
| title_fullStr | New genetic markers for <i>Burkholderia pseudomallei</i> strains typing |
| title_full_unstemmed | New genetic markers for <i>Burkholderia pseudomallei</i> strains typing |
| title_short | New genetic markers for <i>Burkholderia pseudomallei</i> strains typing |
| title_sort | new genetic markers for i burkholderia pseudomallei i strains typing |
| topic | burkholderia pseudomallei genotyping mlva snps phylogeography tandem repeats |
| url | https://iimmun.ru/iimm/article/viewFile/1965/1497 |
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