Acta Scientific Microbiology (ISSN: 2581-3226)

Research Article Volume 4 Issue 11

In Silico Prediction and Comparison of Resistomes in Model Pseudomonas Strains by Resistance Gene Identifier (RGI)

Huayu Qin1, Ming Liu2 and Shiqi Xu1*

1Department of Biomedical Engineering, School of Biomedical Engineering, Chengde Medical University, China
2Department of School of Basic Medical Sciences, Chengde Medical University, China

*Corresponding Author: Shiqi Xu, School of Biomedical Engineering, Chengde Medical University, Shuangqiao District, Chengde Municipality, Hebei Province, China.

Received: October 04, 2021 ; Published: October 21, 2021

×

Abstract

Pseudomonas is a genus of bacteria including strains of human and plant pathogens, plant-growth promoting and biological control agents. While most Pseudomonas strains are known resistant to several antibiotics, their genetic elements conferring antimicrobial resistance (AMR) are largely unexplored systematically. The current study exploits a robust AMR gene predicting tool Resistance Gene Identifier of most recently updated version 5.2.0 based on newly curated database (the Comprehensive Antibiotic Research Database version 3.1.3) to detect AMR genes from thirteen genomes of Pseudomonas strains affiliated with seven species, including twelve pseudomonads as popularly studied model strains plus a well-known Pseudomonas protegens CHA0. A list of 281 AMR genes have been detected in five genomes of Pseudomonas aeruginosa, while 32 in the rest Pseudomonas spp. strains. Among the species, P. aeruginosa, P. fluorescens, P. protegens and P. stutzeri have the resistome of multi-drug resistance, while the rest is resistant to narrower spectrum of drugs. All Pseudomonas spp. investigated here have resistance genes to antibiotics classes of fluoroquinolone and tetracycline, which is consistent with an antibiotic resistance gene hit of adeF (ARO No. 3000777, resistant to fluoroquinolone, tetracycline) has found in high redundancy in almost all Pseudomonas species except P. aeruginosa and P. stutzeri, implying the limit of these classes of drugs for treating pseudomonads. While inter-species data were focused here, further analysis will be conducted to reveal the features of inter-strain level features of pseudomonads. The in silico analysis will complement wet-lab research for designing treating strategies of these bacteria.

Keywords: Pseudomonas; Antimicrobial Resistance; Genome Analysis; Drug Resistance Mechanism; Antibiotic Resistance Gene Ontology

×

References

  1. Alcock B P., et al. "Card 2020: Antibiotic Resistome Surveillance with the Comprehensive Antibiotic Resistance Database”. Nucleic Acids ResearchD1 (2020): D517-D25.
  2. Arango-Argoty G., et al. "Deeparg: A Deep Learning Approach for Predicting Antibiotic Resistance Genes from Metagenomic Data”. Microbiome1 (2018): 23.
  3. Bortolaia, V., et al. "Resfinder 4.0 for Predictions of Phenotypes from Genotypes”. Journal of Antimicrobial Chemotherapy12 (2020): 3491-3500.
  4. Buell C R., et al. "The Complete Genome Sequence of the Arabidopsis and Tomato Pathogen Pseudomonas Syringae Pv. Tomato Dc3000”. Proceedings of the National Academy of Sciences of the United States of America18 (2003): 10181-10186.
  5. Cain A K., et al. "Complete Genome Sequence of Pseudomonas Aeruginosa Reference Strain Pak”. Microbiology Resource Announcements41 (2019).
  6. Collignon P J., et al. "World Health Organization Ranking of Antimicrobials According to Their Importance in Human Medicine: A Critical Step for Developing Risk Management Strategies to Control Antimicrobial Resistance from Food Animal Production”. Clinical Infectious Diseases8 (2016): 1087-1093.
  7. Coyne S., et al. "Overexpression of Resistance-Nodulation-Cell Division Pump Adefgh Confers Multidrug Resistance in Acinetobacter Baumannii”. Antimicrobial Agents and Chemotherapy10 (2010): 4389-4393.
  8. Doster E., et al. "Megares 2.0: A Database for Classification of Antimicrobial Drug, Biocide and Metal Resistance Determinants in Metagenomic Sequence Data”. Nucleic Acids ResearchD1 (2020): D561-D69.
  9. Feldgarden M., et al. "Validating the Amrfinder Tool and Resistance Gene Database by Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of Isolates”. Antimicrobial Agents and Chemotherapy11 (2019).
  10. Gupta S K., et al. "Arg-Annot, a New Bioinformatic Tool to Discover Antibiotic Resistance Genes in Bacterial Genomes”. Antimicrobial Agents and Chemotherapy1 (2014): 212-220.
  11. Hall B G and M Barlow. "Evolution of the Serine Beta-Lactamases: Past, Present and Future”. Drug Resistant Update2 (2004): 111-123.
  12. Jeukens, J., et al. "Comparative Genomics of a Drug-Resistant Pseudomonas Aeruginosa Panel and the Challenges of Antimicrobial Resistance Prediction from Genomes”. FEMS Microbiology Letter18 (2017).
  13. Joardar V., et al. "Whole-Genome Sequence Analysis of Pseudomonas Syringae Pv. Phaseolicola 1448a Reveals Divergence among Pathovars in Genes Involved in Virulence and Transposition”. Journal of Bacteriology18 (2005): 6488-6498.
  14. Kerr K G and A M Snelling. "Pseudomonas Aeruginosa: A Formidable and Ever-Present Adversary”. Journal of Hospital Infection 4 (2009): 338-344.
  15. Magiorakos AP., et al. "Multidrug-Resistant, Extensively Drug-Resistant and Pandrug-Resistant Bacteria: An International Expert Proposal for Interim Standard Definitions for Acquired Resistance”. Clinical Microbiology and Infection3 (2012): 268-281.
  16. Mahmood H Y., et al. "Current Advances in Developing Inhibitors of Bacterial Multidrug Efflux Pumps”. Current Medicinal Chemistry10 (2016): 1062-1081.
  17. Nelson K E., et al. "Complete Genome Sequence and Comparative Analysis of the Metabolically Versatile Pseudomonas Putida Kt2440”. Environmental Microbiology12 (2002): 799-808.
  18. Palleroni N J. "The Pseudomonas Story”. Environmental Microbiology6 (2010): 1377-1383.
  19. Paulsen I T., et al. "Complete Genome Sequence of the Plant Commensal Pseudomonas Fluorescens Pf-5”. Nature Biotechnology7 (2005): 873-878.
  20. Phoenix P., et al. "Characterization of a New Solvent-Responsive Gene Locus in Pseudomonas Putida F1 and Its Functionalization as a Versatile Biosensor”. Environmental Microbiology12 (2003): 1309-1327.
  21. Rowe W P M and M D Winn. "Indexed Variation Graphs for Efficient and Accurate Resistome Profiling”. Bioinformatics 21 (2018): 3601-3608.
  22. Roy P H., et al. "Complete Genome Sequence of the Multiresistant Taxonomic Outlier Pseudomonas Aeruginosa Pa7”. PLoS One1 (2010): e8842.
  23. Schoch C L., et al. "Ncbi Taxonomy: A Comprehensive Update on Curation, Resources and Tools”. Database (Oxford) 2020 (2020).
  24. Silby M W., et al. "Genomic and Genetic Analyses of Diversity and Plant Interactions of Pseudomonas Fluorescens”. Genome Biology5 (2009): R51.
  25. Smits T H M., et al. "Updated Genome Sequence and Annotation for the Full Genome of Pseudomonas Protegens Cha0”. Microbiology Resource Announcements39 (2019).
  26. Stover C K., et al. "Complete Genome Sequence of Pseudomonas Aeruginosa Pao1, an Opportunistic Pathogen”. Nature 6799 (2000): 959-964.
  27. Winstanley C., et al. "Newly Introduced Genomic Prophage Islands Are Critical Determinants of in Vivo Competitiveness in the Liverpool Epidemic Strain of Pseudomonas Aeruginosa”. Genome Research1 (2009): 12-23.
  28. Yan Y., et al. "Nitrogen Fixation Island and Rhizosphere Competence Traits in the Genome of Root-Associated Pseudomonas Stutzeri A1501”. Proceedings of the National Academy of Sciences of the United States of America A 105.21 (2008): 7564-7569.
×

Citation

Citation: Shiqi Xu., et al.In Silico Prediction and Comparison of Resistomes in Model Pseudomonas Strains by Resistance Gene Identifier (RGI)”. Acta Scientific Microbiology 4.11 (2021): 49-55.




Metrics

Acceptance rate33%
Acceptance to publication20-30 days

Indexed In



News and Events


  • Certification for Review
    Acta Scientific certifies the Editors/reviewers for their review done towards the assigned articles of the respective journals.
  • Submission Timeline for Upcoming Issue
    The last date for submission of articles for regular Issues is September 25, 2024.
  • Publication Certificate
    Authors will be issued a "Publication Certificate" as a mark of appreciation for publishing their work.
  • Best Article of the Issue
    The Editors will elect one Best Article after each issue release. The authors of this article will be provided with a certificate of "Best Article of the Issue"
  • Welcoming Article Submission
    Acta Scientific delightfully welcomes active researchers for submission of articles towards the upcoming issue of respective journals.

Contact US