Skip to content
2000
image of Zoonomix: A Pipeline for Assessing Zoonotic Potential and Antibiotic Resistance in Bacterial Genomes

Abstract

Introduction

The increasing emergence of zoonotic pathogens and antimicrobial resistance (AMR) highlights the need for rapid and accurate computational tools to assess the zoonotic potential of bacterial strains. In this study, we present Zoonomix, a bioinformatics pipeline designed to detect and rank genes associated with pathogenicity, virulence, and antibiotic resistance, thereby enabling risk assessment for zoonotic transmission.

Methods

Zoonomix integrates a curated database of ~25,000 genes related to adherence, biofilm formation, efflux pumps, exotoxins, resistance, integrative and conjugative elements (ICEs), and secretion systems (T3SS, T4SS, and T6SS). It uses BLASTN and a scoring algorithm to assess pathogenicity and HGT risk, classifying bacterial strains into low, moderate, or high risk, with insights into antibiotic resistance migration.

Results

When analyzing 60 whole genome sequences of both zoonotic and non-zoonotic bacterial species using the Zoonomix pipeline, over 90% of the results were accurately classified in accordance with existing literature. Notably, the pipeline predicted a potential future zoonotic and pathogenic capability for bacterial species such as and .

Discussion

Zoonomix offers a comprehensive framework for assessing zoonotic potential and antibiotic resistance by integrating genomics, bioinformatics, and predictive analytics. Its ability to detect current gene status, identify mutation-prone genes, summarize mutation hotspots, and flag horizontal gene transfer events make it a valuable tool for disease surveillance and outbreak prevention.

Conclusion

Zoonomix is a scalable, open-source bioinformatics pipeline designed to assess the zoonotic potential and antimicrobial resistance (AMR) risk in bacterial whole genome sequences. By detecting key genes associated with zoonosis, identifying markers that predict the future pathogenic or zoonotic potential of bacteria, and flagging integrative conjugative element (ICEs)-mediated resistance gene transfer mechanisms, the tool provides comprehensive insights into bacterial threats. The pipeline's source code and documentation are freely available for the research community at the following GitHub repository: https://github.com/Umeshkumarku1/ZoonomiX.

© 2025 Bentham Science Publishers
Loading

Article metrics loading...

/content/journals/cbiot/10.2174/0122115501397209251118052633
2025-11-22
2026-02-19

  • From This Site

    /content/journals/cbiot/10.2174/0122115501397209251118052633
    dcterms_title,dcterms_subject,pub_keyword
    -contentType:Contributor -contentType:Concept -contentType:Institution
    10
    5
Loading full text...

Full text loading...

References

  1. Rahman M.T. Sobur M.A. Islam M.S. Zoonotic diseases: Etiology, impact, and control. Microorganisms 2020 8 9 1405 10.3390/microorganisms8091405 32932606
    [Google Scholar]
  2. World Health Organization Regional Office for the Eastern Mediterranean Technical paper on zoonotic diseases and surveillance. 2009 Available from: https://applications.emro.who.int/docs/em_ rc50_7_en.pdf
    [Google Scholar]
  3. Bird B.H. Mazet J.A.K. Detection of emerging zoonotic pathogens: An integrated one health approach. Annu. Rev. Anim. Biosci. 2018 6 1 121 139 10.1146/annurev‑animal‑030117‑014628 29144769
    [Google Scholar]
  4. de Cock M. Fonville M. de Vries A. Screen the unforeseen: Microbiome‐profiling for detection of zoonotic pathogens in wild rats. Transbound. Emerg. Dis. 2022 69 6 3881 3895 10.1111/tbed.14759 36404584
    [Google Scholar]
  5. Rolfe R.J. Sheldon S.W. Kingry L.C. Metagenomic detection of bacterial zoonotic pathogens among febrile patients, Tanzania, 2007–20091. Emerg. Infect. Dis. 2024 30 8 1599 1608 10.3201/eid3008.240529 39043406
    [Google Scholar]
  6. Qi Y. Li Y. Wang J. Lu N. Lv R. Recombinase polymerase amplification for rapid detection of zoonotic pathogens: An overview. Zoonoses 2022 2 1 990 10.15212/ZOONOSES‑2022‑0002
    [Google Scholar]
  7. Hu RS Zhang X Wei Y ZooPathWeb: A comprehensive web resource for zoonotic pathogens. Bioinformatics Advances 2023 3 1 vbad094 10.1093/bioadv/vbad094
    [Google Scholar]
  8. National Library of Medicine. Homo sapiens FYN binding protein 1 (FYB1), transcript variant 4, mRNA. Available from: https://www.ncbi.nlm.nih.gov/nuccore/NM_001349333.1
  9. Olson R.D. Assaf R. Brettin T. Introducing the bacterial and viral bioinformatics resource center (BV-BRC): A resource combining PATRIC, IRD and ViPR. Nucleic Acids Res. 2023 51 D1 D678 D689 10.1093/nar/gkac1003 36350631
    [Google Scholar]
  10. Liu M. Li X. Xie Y. ICEberg 2.0: An updated database of bacterial integrative and conjugative nlms. Nucleic Acids Res. 2019 47 D1 D660 D665 10.1093/nar/gky1123 30407568
    [Google Scholar]
  11. Bortolaia V. Kaas R.S. Ruppe E. ResFinder 4.0 for predictions of phenotypes from genotypes. J. Antimicrob. Chemother. 2020 75 12 3491 3500 10.1093/jac/dkaa345 32780112
    [Google Scholar]
  12. Clausen P.T.L.C. Aarestrup F.M. Lund O. Rapid and precise alignment of raw reads against redundant databases with KMA. BMC Bioinformatics 2018 19 1 307 10.1186/s12859‑018‑2336‑6 30157759
    [Google Scholar]
  13. Chen L. Yang J. Yu J. VFDB: A reference database for bacterial virulence factors. Nucleic Acids Res. 2004 33 Database issue D325 D328 10.1093/nar/gki008 15608208
    [Google Scholar]
  14. Pugazhendhi A.S. Wei F. Hughes M. Coathup M. Bacterial adhesion, virulence, and biofilm formation. Musculoskeletal Infection. Coathup M. Cham Springer International Publishing 2022 19 64 10.1007/978‑3‑030‑83251‑3_2
    [Google Scholar]
  15. Hajiagha M.N. Kafil H.S. Efflux pumps and microbial biofilm formation. Infect. Genet. Evol. 2023 112 105459 10.1016/j.meegid.2023.105459 37271271
    [Google Scholar]
  16. Botelho J. Schulenburg H. The role of integrative and conjugative nlms in antibiotic resistance evolution. Trends Microbiol. 2021 29 1 8 18 10.1016/j.tim.2020.05.011 32536522
    [Google Scholar]
  17. Green ER Mecsas J Bacterial secretion systems: An overview. Microbiol Spectr 2016 4 1 VMBF-0012-2015 10.1128/microbiolspec.VMBF‑0012‑2015 26999395
    [Google Scholar]
  18. Hirakawa H. Suzue K. Takita A. Tomita H. Roles of OmpA in type III secretion system-mediated virulence of Enterohemorrhagic Escherichia coli. Pathogens 2021 10 11 1496 10.3390/pathogens10111496 34832651
    [Google Scholar]
  19. Coburn B. Sekirov I. Finlay B.B. Type III secretion systems and disease. Clin. Microbiol. Rev. 2007 20 4 535 549 10.1128/CMR.00013‑07 17934073
    [Google Scholar]
  20. Confer AW Ayalew S The OmpA family of proteins: Roles in bacterial pathogenesis and immunity. Vet Microbiol 2013 163 3-4 207 22 10.1016/j.vetmic.2012.08.019 22986056
    [Google Scholar]
  21. Battistoni A. Role of prokaryotic Cu,Zn superoxide dismutase in pathogenesis. Biochem. Soc. Trans. 2003 31 6 1326 1329 10.1042/bst0311326 14641055
    [Google Scholar]
  22. Juhas M. Crook D.W. Hood D.W. Type IV secretion systems: Tools of bacterial horizontal gene transfer and virulence. Cell. Microbiol. 2008 10 12 2377 2386 10.1111/j.1462‑5822.2008.01187.x 18549454
    [Google Scholar]
  23. Wozniak R.A.F. Waldor M.K. Integrative and conjugative nlms: Mosaic mobile genetic nlms enabling dynamic lateral gene flow. Nat. Rev. Microbiol. 2010 8 8 552 563 10.1038/nrmicro2382 20601965
    [Google Scholar]
  24. Johnson C.M. Grossman A.D. Integrative and Conjugative nlms (ICEs): What they do and how they work. Annu. Rev. Genet. 2015 49 1 577 601 10.1146/annurev‑genet‑112414‑055018 26473380
    [Google Scholar]
  25. Bellanger X. Payot S. Leblond-Bourget N. Guédon G. Conjugative and mobilizable genomic islands in bacteria: Evolution and diversity. FEMS Microbiol. Rev. 2014 38 4 720 760 10.1111/1574‑6976.12058 24372381
    [Google Scholar]
  26. Partridge S.R. Kwong S.M. Firth N. Jensen S.O. Mobile genetic nlms associated with antimicrobial resistance. Clin. Microbiol. Rev. 2018 31 4 e00088 e17 10.1128/CMR.00088‑17 30068738
    [Google Scholar]
  27. Frost L.S. Leplae R. Summers A.O. Toussaint A. Mobile genetic nlms: The agents of open source evolution. Nat. Rev. Microbiol. 2005 3 9 722 732 10.1038/nrmicro1235 16138100
    [Google Scholar]
  28. Roberts A.P. Mullany P. Oral biofilms: A reservoir of transferable, bacterial, antimicrobial resistance. Expert Rev. Anti Infect. Ther. 2010 8 12 1441 1450 10.1586/eri.10.106 21133668
    [Google Scholar]
  29. Li J O'Toole PW Disease-associated microbiome signature species in the gut. PNAS Nexus 2024 3 9 pgae352 10.1093/pnasnexus/pgae352 39228810
    [Google Scholar]
  30. Stringer O.W. Li Y. Bossé J.T. Langford P.R. JMM Profile: Actinobacillus pleuropneumoniae: A major cause of lung disease in pigs but difficult to control and eradicate. J. Med. Microbiol. 2022 71 3 001483 10.1099/jmm.0.001483 35262474
    [Google Scholar]
  31. Guo F. Quan R. Cui Y. Cao X. Wen T. Xu F. Effects of OxyR regulator on oxidative stress, Apx toxin secretion and virulence of Actinobacillus pleuropneumoniae. Front. Cell. Infect. Microbiol. 2024 13 1324760 10.3389/fcimb.2023.1324760 38268788
    [Google Scholar]
  32. Ogunleye S.C. Olorunshola M.M. Fasina K.A. Anthrax outbreak: Exploring its biological agents and public health implications. Front Trop Dis 2024 4 1297896 10.3389/fitd.2023.1297896
    [Google Scholar]
  33. Ferris A.M. Dawson D.G. Eyler A.B. Bacillus cereus biovar anthracis causes inhalational anthrax-like disease in rabbits that is treatable with medical countermeasures. PLoS Negl. Trop. Dis. 2025 19 4 e0012973 10.1371/journal.pntd.0012973 40193393
    [Google Scholar]
  34. Boulouis H.J. Chao-chin C. Henn J.B. Kasten R.W. Chomel B.B. Factors associated with the rapid emergence of zoonotic Bartonella infections. Vet. Res. 2005 36 3 383 410 10.1051/vetres:2005009 15845231
    [Google Scholar]
  35. Osborne A.J. Clark S.E. Whitcomb T. Devlin P. Lanza M. Atkins H.M. Unique presentations of Burkholderia gladioli infections in several strains of immunocompromised mice. Comp. Med. 2023 73 5 391 397 10.30802/AALAS‑CM‑23‑000016 38087404
    [Google Scholar]
  36. Rasetti-Escargueil C. Lemichez E. Popoff M.R. Public health risk associated with botulism as foodborne zoonoses. Toxins 2019 12 1 17 10.3390/toxins12010017 31905908
    [Google Scholar]
  37. Hu J. Afayibo D.J.A. Zhang B. Characteristics, pathogenic mechanism, zoonotic potential, drug resistance, and prevention of avian pathogenic Escherichia coli (APEC). Front. Microbiol. 2022 13 1049391 10.3389/fmicb.2022.1049391 36583051
    [Google Scholar]
  38. Kant R. Paulin L. Alatalo E. de Vos W.M. Palva A. Genome sequence of Lactobacillus amylovorus GRL1112. J. Bacteriol. 2011 193 3 789 790 10.1128/JB.01365‑10 21131492
    [Google Scholar]
  39. de Jesus L.C.L. de Jesus Sousa T. Coelho-Rocha N.D. Safety evaluation of Lactobacillus delbrueckii subsp. lactis CIDCA 133: A health-promoting bacteria. Probiotics Antimicrob. Proteins 2022 14 5 816 829 10.1007/s12602‑021‑09826‑z 34403080
    [Google Scholar]
  40. Končurat A. Sukalić T. Listeriosis: Characteristics, occurrence in domestic animals, public health significance, surveillance and control. Microorganisms 2024 12 10 2055 10.3390/microorganisms12102055 39458364
    [Google Scholar]
  41. Rice J.A. Carrasco-Medina L. Hodgins D.C. Shewen P.E. Mannheimia haemolytica and bovine respiratory disease. Anim. Health Res. Rev. 2007 8 2 117 128 10.1017/S1466252307001375 18218156
    [Google Scholar]
  42. Woldemariam T. Mohammed T. Zewude A. Zoonotic transmission of the Mycobacterium tuberculosis complex between cattle and humans in Central Ethiopia. Front. Vet. Sci. 2025 12 1527279 10.3389/fvets.2025.1527279 40129575
    [Google Scholar]
  43. Rao R.T. Madhavan V. Kumar P. Muniraj G. Sivakumar N. Kannan J. Epidemiology and zoonotic potential of Livestock-associated Staphylococcus aureus isolated at Tamil Nadu, India. BMC Microbiol. 2023 23 1 326 10.1186/s12866‑023‑03024‑3 37923998
    [Google Scholar]
  44. Inzana T.J. Virulence properties of Actinobacillus pleuropneumoniae. Microb. Pathog. 1991 11 5 305 316 10.1016/0882‑4010(91)90016‑4 1816486
    [Google Scholar]
  45. Ziarati M. Zorriehzahra M.J. Hassantabar F. Zoonotic diseases of fish and their prevention and control. Vet. Q. 2022 42 1 95 118 10.1080/01652176.2022.2080298 35635057
    [Google Scholar]
  46. Dewi G. Kollanoor Johny A. Lactobacillus in food animal production— A forerunner for clean label prospects in animal-derived products. Front. Sustain. Food Syst. 2022 6 831195 10.3389/fsufs.2022.831195
    [Google Scholar]
  47. Deng Y. Xu H. Su Y. Horizontal gene transfer contributes to virulence and antibiotic resistance of Vibrio harveyi 345 based on complete genome sequence analysis. BMC Genomics 2019 20 1 761 10.1186/s12864‑019‑6137‑8 31640552
    [Google Scholar]
  48. Zuryn S. Le Gras S. Jamet K. Jarriault S. A strategy for direct mapping and identification of mutations by whole-genome sequencing. Genetics 2010 186 1 427 430 10.1534/genetics.110.119230 20610404
    [Google Scholar]
  49. Cosentino S. Larsen M.V. Aarestrup F.M. Lund O. PathogenFinder--Distinguishing friend from foe using bacterial whole genome sequence data. PLoS One 2013 8 10 e77302 10.1371/journal.pone.0077302 24204795
    [Google Scholar]
  50. Tausch S.H. Loka T.P. Schulze J.M. PathoLive—Real-Time pathogen identification from metagenomic illumina datasets. Life 2022 12 9 1345 10.3390/life12091345 36143382
    [Google Scholar]
  51. Djordjevic S.P. Jarocki V.M. Seemann T. Genomic surveillance for antimicrobial resistance — A one health perspective. Nat. Rev. Genet. 2024 25 2 142 157 10.1038/s41576‑023‑00649‑y 37749210
    [Google Scholar]
/content/journals/cbiot/10.2174/0122115501397209251118052633
Loading
Zoonomix: A Pipeline for Assessing Zoonotic Potential and Antibiotic Resistance in Bacterial Genomes
Bentham Science Publishers ; https://doi.org/10.2174/0122115501397209251118052633
/content/journals/cbiot/10.2174/0122115501397209251118052633
/content/journals/cbiot/10.2174/0122115501397209251118052633
Loading

Data & Media loading...


  • Article Type:     Research Article
Keywords: virulence factors ; bacterial genomics ; Zoonomix ; zoonotic pathogens ; horizontal gene transfer ; bioinformatics pipeline

Most Cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error
Please enter a valid_number test