Metagenomic analysis to identify the causative agents of atypical urogenital tract infections

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Abstract

Background. Research in recent decades has shown that classical microbiological methods can only detect a small, cultivable portion of microorganisms. One of the modern approaches to detect a wide range of bacteria and archaea is presented as a type of metagenomic analysis performed by high-throughput sequencing of ribosomal operon fragment libraries. Objective is to conduct metagenomic analysis of samples from the urogenital tract of patients with chronic inflammation to identify pathogens not detected by other methods. Methods. Taxonomic analysis of the bacterial community was performed by high-throughput sequencing of the V3–V4 hypervariable region of the 16S rRNA gene by using the Illumina HiSeq 3000 platform. Results. The study allowed to identify the taxonomic diversity of microorganisms in samples from the urogenital tract (from 197 to 794 different microorganisms belonging to the Bacteria were identified), as well as to establish differential differences concerning members of the genera Megasphaera, Prevotella, Veillonella, Pedobacter, Mobiluncus, Phobormidium, Sphing Temperatibacter, Oxobacter, Georgenia, Actinobaculum, Varibaculum, Mycobacterium, Rhodococcus, Sediminihabitans, Actinobacter, Actinoplanes, Spirochaeta, Enhydrobacter, Thermacetogenium, Bdellovibrio, Oleibacter, Porphyromonas, Klebsiella, Lachnoclostridium, Caulobacter, Xanthomonas, Novispirillum, Marvinbryantia, Afipia, Shinella, Tepidimonas, Faecalibacterium, Paludibacterium, Aerococcus, Campylobacter, Pasteurella, Rumen, Psychrobacter, Haemophilus, Brevibacillus, Sporosarcina, Yaniella and Lactobacillus between samples from patients with chronic inflammation and apparently healthy individuals. Conclusion. Differential differences were found in the composition of the microbiome from the samples of patients with chronic inflammation and apparently healthy individuals, concerning members of 44 genera, including Megasphaera, Prevotella, Veillonella, Pedobacter, Mobiluncus, Phormidium and Lactobacillus. The inflammatory processes observed in the patient urogenital tract can be associated with imbalanced microflora such as decreased level of typical members of the genera Staphylococcus, Streptococcus and Lactobacillus, but increased number of members from of the genera Klebsiella and Citrobacter.

About the authors

D. S. Kutilin

National Medical Research Oncology Center, Rostov-on-Don, Russian Federation

Author for correspondence.
Email: k.denees@yandex.ru
ORCID iD: 0000-0002-8942-3733

Denis S. Kutilin - PhD (Biology), Leading Researcher, Laboratory of Molecular Oncology, National Medical Research Oncology Center, Rostov-on-Don, Russian Federation.

344037, Rostov-on-Don, Liniya 14 str., 63.

Phone: +7 951 538-50-39

Russian Federation

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