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. 2024 Dec 8;25(23):13200.
doi: 10.3390/ijms252313200.

Biochip-Based Identification of Mycobacterial Species in Russia

Danila Zimenkov  1 , Vyacheslav Zhuravlev  2 , Anastasia Ushtanit  1 , Marina Filippova  1 , Uliana Semenova  1 , Natalia Solovieva  2 , Maria Sviridenko  3 , Anastasia Khakhalina  3 , Svetlana Safonova  3 , Marina Makarova  3 , Elizaveta Gordeeva  4 , Elena Guselnikova  4 , Yakov Schwartz  4 , Natalia Stavitskaya  4 , Peter Yablonsky  2
Affiliations

Biochip-Based Identification of Mycobacterial Species in Russia

Danila Zimenkov et al. Int J Mol Sci. .

Abstract

Infections caused by nontuberculous mycobacteria (NTM) are rising globally throughout the world. The number of species isolated from clinical samples is steadily growing, which demands the implementation of a robust diagnostic method with wide specificity. This study was carried out in in 2022-2024 in three clinical antituberculosis centers in the biggest cities of Russia: Moscow, Saint Petersburg, and Novosibirsk. We developed the DNA hybridization assay 'Myco-biochip' that allows the identification of 79 mycobacterial species and analyzed 3119 samples from 2221 patients. Sixty-eight mycobacterial species were identified in clinics, including the three novel species phylogenetically related to M. duvalii, M. lentiflavum, and M. talmoniae. The identification of a close relative of M. talmoniae adds to the existence of separate clade between M. terrae, M. triviale complexes and other slow-growing Mycobacteria, which supports the thesis against the splitting of Mycobacteria into five separate genera. Adding to the list of potentially pathogenic species, we identified M. adipatum and M. terramassiliense, which were previously described as natural habitats. The diversity of acid-fast bacilli identified in TB-suspected persons was not limited to the Mycobacteria genus and also includes species from genera Nocardia, Gordonia, Corynebacterium, Tsukamurella, and Rhodococcus of the order Mycobacteriales. The revealed bacterial diversity in patients with suspected NTM-diseases requires the implementation of relevant species identification assays as the first step in the laboratory diagnostic pipeline.

Keywords: M. moscowiensis; M. petersburgensis; M. sibiricum; NTM; biochip; mycobacteria; nontuberculous mycobacteria; oligonucleotide array.

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Conflict of interest statement

The authors declare no conflicts of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.

Figures

Figure 1
Figure 1
Myco-biochip layout scheme and examples of hybridization patterns. The list of oligonucleotide probes with designation used is given in the Supplementary Materials.
Figure 2
Figure 2
Frequency of Mycobacteria species in patients with TB-like disease in Russia. The phylogenetic tree was constructed on the basis of pairwise amino acid identity (AAI) calculation. The squares of callout bubbles are proportional to the number of clinical cases. The novel mycobacterial species identified in the study are given in bold. An additional 11 species that could be identified by Myco-biochip are marked with triangles.
Figure 3
Figure 3
Regional differences in the spectra of NTM isolation in the Russian Federation. Only regions with a significant number of cases were analyzed. The three TB centers responsible for the collection and processing of clinical samples are shown with yellow circles.
See this image and copyright information in PMC

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