Comparative Analysis of Proteomes of a Number of Nosocomial Pathogens by KEGG Modules and KEGG Pathways
Abstract
:1. Introduction
2. Results and Discussion
2.1. Comparison of Single Genomes of S. aureus, E. cloacae, P. aeruginosa, M. mobile
2.2. Analysis of Pangenomes and Core Genomes
2.2.1. S. aureus
2.2.2. Enterobacter spp.
2.2.3. P. aeruginosa
2.2.4. Mycoplasma spp.
2.3. Comparison of Core Genomes and Pangenomes
3. Materials and Methods
3.1. KEGG Databases
3.2. Organisms of Interest
- Staphylococcus aureus. Reference strain NCTC 8325, 53 genomes of S. aureus were used.
- Enterobacter species. Reference strain EcWSU1, 35 genomes of Enterobacter spp. were used.
- Pseudomonas aeruginosa. Reference strain ATCC 15692, 21 genomes of P. aeruginosa were used.
- Mycoplasma species. Reference strain ATCC 43663, 92 genomes of Mycoplasma spp. were used.
3.3. Algorithm of Comparison
4. Conclusions
- (1)
- Each S. aureus strain has multidrug resistance systems, even if they are susceptible to methicillin. Twenty-five percent of the strains in the KEGG database are methicillin resistant, 85% of the strains are tetracycline resistant, 45% of the strains have the beta-lactam resistance module, and 21% of the genomes have the QacA efflux system multidrug resistance module.
- (2)
- Enterobacter spp. have a wide range of antibiotic resistance systems, however, there are strains without such systems at all. Seventy-six percent of the strains have at least one such system. Twenty-one percent of the Enterobacter spp. strains in the KEGG database are resistant to carbapenems. Seventy-four percent of the strains have the AcrEF-TolC efflux system module.
- (3)
- P. aeruginosa has a wide range of unique efflux systems. One hundred percent of the strains have at least two drug resistance systems, and 75% of the strains have seven. Resistance to carbapenems was found in 14% of the strains. The M00718 module of the MexAB-OprM efflux system, which confers multidrug resistance, and the M00745 module of the OprD repression system, conferring resistance to imipenem, were found in 20 of the 21 genomes.
- (4)
- Mycoplasma spp. do not have annotated antibiotic resistance or antimicrobial peptide resistance modules, although resistance has been proven for some Mycoplasma species. Determination of resistance mechanisms requires additional research.
- (5)
- Each of the organisms has a characteristic set of metabolic traits, whose contribution to drug resistance can be determined in future studies.
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
Abbreviations
AMP | Antimicrobial peptide |
MDR | Multidrug resistance |
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Protein Genes | RNA Genes | KEGG Modules | KEGG Pathways | |
---|---|---|---|---|
S. aureus | 2767 | 77 | 105 | 104 |
E. cloacae | 4619 | 108 | 208 | 118 |
P. aeruginosa | 5572 | 106 | 165 | 121 |
M. mobile | 635 | 34 | 17 | 52 |
Total | Drug Resistance | Metabolic | Transport | Regulation | AMP Resistance | |
---|---|---|---|---|---|---|
S | 38 | 7 | 6 | 12 | 10 | 3 |
P | 48 | 10 | 14 | 11 | 13 | 0 |
E | 75 | 5 | 27 | 30 | 9 | 4 |
EP | 65 | 5 | 24 | 26 | 10 | 1 |
SE | 12 | 0 | 3 | 9 | 0 | 0 |
EM | 1 | 0 | 1 | 0 | 0 | 0 |
SEP | 39 | 0 | 26 | 11 | 2 | 0 |
SEM | 3 | 0 | 1 | 2 | 0 | 0 |
SEPM | 13 | 0 | 9 | 4 | 0 | 0 |
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Slizen, M.V.; Galzitskaya, O.V. Comparative Analysis of Proteomes of a Number of Nosocomial Pathogens by KEGG Modules and KEGG Pathways. Int. J. Mol. Sci. 2020, 21, 7839. https://doi.org/10.3390/ijms21217839
Slizen MV, Galzitskaya OV. Comparative Analysis of Proteomes of a Number of Nosocomial Pathogens by KEGG Modules and KEGG Pathways. International Journal of Molecular Sciences. 2020; 21(21):7839. https://doi.org/10.3390/ijms21217839
Chicago/Turabian StyleSlizen, Mikhail V., and Oxana V. Galzitskaya. 2020. "Comparative Analysis of Proteomes of a Number of Nosocomial Pathogens by KEGG Modules and KEGG Pathways" International Journal of Molecular Sciences 21, no. 21: 7839. https://doi.org/10.3390/ijms21217839