2026 / 05

DOI: 10.24075/brsmu.2026.052
Copyright: © 2026 by the authors. Licensee: Pirogov University.
This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (CC BY).

ORIGINAL RESEARCH

Phylogenetic and functional genomic heterogeneity of Bordetella bronchiseptica isolates from culture collections

Asmaeva PV2 , Borisova OYu1,2 , Pimenova AS1 , Andrievskaya IYu1 , Chaplin AV1,2 , Kafarskaya LI1 , Efimov BA1 , Evseev PV1,2
About authors

1 Gabrichevsky Research Institute for Epidemiology and Microbiology, Moscow, Russia

2 Pirogov Russian National Research Medical University, Moscow, Russia

Correspondence should be addressed: Polina V. Asmaeva
Ostrovityanova, 1, Moscow, 117997, Russia; moc.liamg@91aveamsa

About paper

Funding: the study was conducted within the framework of a dedicated Rospotrebnadzor program.

Author contribution: Asmaeva PV, Chaplin AV — phylogenomic and phylogenetic analysis, comparative genomic analysis, data analysis, manuscript preparation; Borisova OYu — study design, data analysis, manuscript preparation; Pimenova AS, Andrievskaya IYu — microscopic, bacteriological, mass spectrometric and molecular genetic studies, preparation of the manuscript; Kafarskaya LI — data analysis; Efimov BA — manuscript preparation; Evseev PV — data analysis, manuscript preparation.

Received: 2026-08-12 Accepted: 2026-09-12 Published online: 2026-09-27
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  1. Bouchez V, Guglielmini J, Dazas M, et al. Genomic Sequencing of Bordetella pertussis for Epidemiology and Global Surveillance of Whooping Cough. Emerging Infectious Diseases. 2018; 24 (6): 988–94. https://doi.org/10.3201/eid2406.171464.
  2. Bridel S, Bouchez V, Brancotte B, et al. A Comprehensive Resource for Bordetella Genomic Epidemiology and Biodiversity Studies. Nature Communications. 2022; 13 (1): 3807. https://doi.org/10.1038/s41467-022-31517-8.
  3. Linz B, Ivanov YV, Preston A, et al. Acquisition and Loss of Virulence-Associated Factors during Genome Evolution and Speciation in Three Clades of Bordetella Species. BMC Genomics. 2016; 17 (1): 767. https://doi.org/10.1186/s12864-016-3112-5.
  4. Park J, Zhang Y, Buboltz AM, et al. Comparative Genomics of the Classical Bordetella Subspecies: The Evolution and Exchange of Virulence-Associated Diversity amongst Closely Related Pathogens. BMC Genomics. 2012; 13 (1): 545. https://doi.org/10.1186/1471-2164-13-545.
  5. Liu Junqi, Xiaofeng Zheng, Chenghao Jia, et al. Zoonotic Bordetella bronchiseptica Infection at the Swine-Human Interface: Unveiling the Evolutionary Path from an Animal to a Human Pathogen. Emerging Microbes & Infections. 2026; 15 (1): 2637286. https://doi.org/10.1080/22221751.2026.2637286.
  6. Chen Qing, Gray MC, Hewlett E, Stibitz S. Four Single-Basepair Mutations in the Ptx Promoter of Bordetella bronchiseptica Are Sufficient to Activate the Expression of Pertussis Toxin. Scientific Reports. 2021; 11 (1): 9373. https://doi.org/10.1038/s41598-021-88852-x.
  7. Kloos WE, Mohapatra N, Dobrogosz WJ, Ezzell JW, Manclark CR. Deoxyribonucleotide Sequence Relationships Among Bordetella Species. International Journal of Systematic Bacteriology. 1981; 31 (2): 173–76. https://doi.org/10.1099/00207713-31-2-173.
  8. Cummings CA, Brinig MM, Lepp PW, Van De Pas S, Relman DA. Bordetella Species Are Distinguished by Patterns of Substantial Gene Loss and Host Adaptation. Journal of Bacteriology. 2004; 186 5: 1484–92. https://doi.org/10.1128/JB.186.5.1484-1492.2004.
  9. Parkhill J, Sebaihia M, Preston A, et al. Comparative Analysis of the Genome Sequences of Bordetella Pertussis, Bordetella Parapertussis and Bordetella bronchiseptica. Nature Genetics. 2003; 35 (1): 32–40. https://doi.org/10.1038/ng1227.
  10. Diavatopoulos DA, Cummings CA, Schouls LM, Brinig MM, Relman DA, Mooi FR. Bordetella Pertussis, the Causative Agent of Whooping Cough, Evolved from a Distinct, Human-Associated Lineage of B. bronchiseptica. PLoS Pathogens. 2005; 1 (4): e45. https://doi.org/10.1371/journal.ppat.0010045.
  11. Chen S, et al. Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018; 34: i884–i890. DOI: 10.1093/bioinformatics/bty560.
  12. Wick RR, et al. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol. 2017; 13: e1005595. DOI: 10.1371/journal.pcbi.1005595.
  13. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013; 29 (8): 1072–5. DOI: 10.1093/bioinformatics/btt086.
  14. Chklovski A, et al. CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nat Methods. 2023; 20: 1203–12. DOI: 10.1038/s41592-023-01940-w.
  15. Schwengers O, et al. Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microb Genom. 2021; 7: 000685. DOI: 10.1099/mgen.0.000685.
  16. Lee I, et al. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol. 2016; 66: 1100–03. DOI: 10.1099/ijsem.0.000760.
  17. Chaumeil P-A, et al. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics. 2020; 36: 1925–7. DOI: 10.1093/bioinformatics/btz848.
  18. Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S, Madden TL. NCBI BLAST: a better web interface. Nucleic Acids Research. 2008; 36 (Web Server issue): W5–W9. DOI: 10.1093/nar/gkn201.
  19. Li X, Hu Y, Gong J, Zhang L, Wang G. Comparative genome characterization of Achromobacter members reveals potential genetic determinants facilitating the adaptation to a pathogenic lifestyle. Applied Microbiology and Biotechnology. 2013; 97 (14): 6413–25. DOI: 10.1007/s00253-013-5018-3.
  20. Weigand MR, Peng Y, Batra D, et al. Conserved Patterns of Symmetric Inversion in the Genome Evolution of Bordetella Respiratory Pathogens. mSystems. 2019; 4 (6): e00702-19. DOI: 10.1128/mSystems.00702-19.
  21. Kim J, et al. UBCG2: Up-to-date bacterial core genes and pipeline for phylogenomic analysis. J Microbiol. 2021; 59: 609–15. DOI: 10.1007/s12275-021-1231-4.
  22. Katoh K, Standley DM. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Mol Biol Evol. 2013; 30: 772–80. DOI: 10.1093/molbev/mst010.
  23. Borowiec ML. AMAS: a fast tool for alignment manipulation and computing of summary statistics. PeerJ. 2016; 4: e1660. DOI: 10.7717/peerj.1660.
  24. Minh BQ, et al. IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. Mol Biol Evol. 2020; 37: 1530–4. DOI: 10.1093/molbev/msaa015.
  25. Letunic I, Bork P. Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool. Nucleic Acids Res. 2024; 52: W78–W82. DOI: 10.1093/nar/gkae268.
  26. Seemann T. ABRicate, Github. Available from: https://github.com/tseemann/abricate.
  27. Payne LJ, et al. Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types. Nucleic Acids Res. 2021; 49: 10868–78. DOI: 10.1093/nar/gkab883.
  28. Wishart DS, et al. PHASTEST: faster than PHASTER, better than PHAST. Nucleic Acids Res. 2023; 51: W443–W450. DOI: 10.1093/nar/gkad382.
  29. Starikova EV, et al. Phigaro: high-throughput prophage sequence annotation. Bioinformatics. 2020; 36: 3882–4. DOI: 10.1093/bioinformatics/btaa250.
  30. Eren AM, et al. Community-led, integrated, reproducible multi-omics with anvi'o. Nat Microbiol. 2021; 6: 3–6. DOI: 10.1038/s41564-020-00834-3.