Experience of applying the metagenomic sequencing method on fragments of the <i>16S</i> rRNA gene for the detection and identification of natural focal infection pathogens
Introduction. Metagenomic sequencing is one of the most promising methods for both the detection and identification of natural focal infection (NFI) pathogens and for determining the species composition of various bacterial communities. The aim is to detect and identify the NFI pathogens in sample...
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| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | Russian |
| Published: |
Central Research Institute for Epidemiology
2025-05-01
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| Series: | Журнал микробиологии, эпидемиологии и иммунобиологии |
| Subjects: | |
| Online Access: | https://microbiol.crie.ru/jour/article/viewFile/18828/1592 |
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| Summary: | Introduction. Metagenomic sequencing is one of the most promising methods for both the detection and identification of natural focal infection (NFI) pathogens and for determining the species composition of various bacterial communities.
The aim is to detect and identify the NFI pathogens in samples of field and clinical material using metagenomic sequencing of 16S rRNA gene fragments, and to analyze the taxonomic composition of endosymbiotic microorganisms in the samples.
Materials and methods. Samples of field (14 samples) and clinical (2 samples) material with varying loads of DNA from NFI pathogens, determined by PCR (Borrelia burgdorferi sensu lato, Anaplasma phagocytophilum, Francisella tularensis, Rickettsia spp., Coxiella burnetii), were investigated. Amplification of fragments of the gene encoding 16S rRNA was performed using primers flanking the variable regions of the gene.
Results. In 14 out of 16 studied samples, target NFI pathogens were detected. The species identified included R. aeschlimannii (in 57.1% of positive samples), B. valaisiana (in 16.6%), F. tularensis (in 75%), C. burnetii (in 100%), and borreliae — pathogens of relapsing fevers (B. turcica, B. hispanica) were also found in one sample. The taxonomic structure of the microbiome of Ixodes ricinus, Dermacentor reticulatus, Rhipicephalus annulatus, Hyalomma aegyptium, Dermacentor marginatus ticks collected in the southern regions of the Russian Federation was studied. It was shown that the predominant microorganisms are representatives of the genera Flavobacterium, Pseudomonas, Serratia, Aeromonas, Pedobacter, Bradyrhizobium, Shingomonas. DNA markers of microorganisms — endosymbionts of ticks Candidatus Midichloria mitochondrii, representatives of the genera Rickettsiella, Coxiella, non-pathogenic and conditionally pathogenic species of the genus Francisella were found in pools of Ixodes ticks.
Conclusion. The effectiveness of the method of metagenomic sequencing of fragments of the 16S rRNA gene for the detection and identification of NFI pathogens in samples of clinical and field material was demonstrated. Metagenomic sequencing of 16S rRNA gene regions can be recommended as an additional laboratory method for detecting and identifying NFI pathogens. |
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| ISSN: | 0372-9311 2686-7613 |