Investigating the OXA Variants of ESKAPE Pathogens
Abstract
:1. Introduction
2. Results and Discussion
2.1. Data Statistics and Classification of ESKAPE Pathogens
2.2. Construction of Profile HMM of BlaOXA
2.3. Distribution and Localization of BlaOXA in ESKAPE Pathogens
2.4. Classification of BlaOXA Variants in Subfamilies
2.5. Identification of Relatedness among BlaOXA
2.6. Analysis of Amino Acid Variations in OXA Subfamilies
2.7. Pairwise Identity between the Subfamilies
2.8. Amino Acid Analysis of Representatives of OXA Subfamilies and Their Phylogenetic Study
2.9. Structural Variations in the 3D Protein Models of the OXA Subfamilies
3. Materials and Methods
3.1. Data Collection
3.2. Building Profile HMM and OXA Search in the Genomes of ESKAPE Pathogens
3.3. Multiple Sequence Alignment and Phylogenetic Tree
3.4. Determination of Pairwise Sequence Identity in Representatives of OXA Subfamilies and Phylogenetic Analysis
3.5. 3D Modeling and Assessment of Structural Variations in the OXA Subfamilies
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
OXA | Oxacillinases |
ESKAPE | Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species |
WHO | World Health Organization |
AMR | Antimicrobial Resistance |
MDR | Multidrug Resistance |
blaOXA | OXA β-lactamase |
ARG | Antibiotic Resistance Gene |
MSA | Multiple Sequence Alignment |
HMM | Hidden Markov Model |
RMSD | Root Mean Square Deviation |
CBMAR | Comprehensive Beta-lactamase Molecular Annotation Resource |
NCBI | National Center for Biotechnology Information |
NR | Non Redundant |
BLDB | Beta-Lactamase Database |
NJ | Neighbor joining |
BLAST | Basic Local Alignment Search Tool |
BEAST | Bayesian evolutionary analysis through a simple tutorial |
BEAUti | Bayesian Evolutionary Analysis Utility |
MCMC | Markov chain Monte Carlo |
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Organism | Total No. of Genomes (NCBI) | No. of Complete Genomes/No. of blaOXA | Replicons | |||
---|---|---|---|---|---|---|
No. of Chromosomal Genomes/No. of blaOXA | Both Chromosome and Plasmid | |||||
No. of Genomes Containing Both Chromosomes and Plasmids/No. of blaOXA (Total) | No. of Chromosomes/No. of blaOXA | No. of Plasmids/No. of blaOXA | ||||
E. faecium | 2256 | 187/0 | 12/0 | 175/0 | 175/0 | 851/0 |
S. aureus | 12,397 | 590/0 | 285/0 | 305/0 | 305/0 | 467/0 |
K. pneumoniae | 10,383 | 732/263 | 63/6 | 669/257 | 669/39 | 2362/218 |
A. baumannii | 5057 | 233/408 | 50/82 | 183/326 | 183/283 | 384/43 |
P. aeruginosa | 5711 | 291/235 | 254/199 | 37/36 | 37/25 | 50/11 |
Enterobacter spp. | 2680 | 225/23 | 53/0 | 172/23 | 172/4 | 593/19 |
Total | 2258/929 | 717/287 | 1541/642 | 1541/351 | 4707/291 |
S. No. | Enzyme Group | Organism and Gene Location(s) | Number of Sequences | Variations |
---|---|---|---|---|
1 | OXA-48-like | K. pneumoniae (B: chromosome, B: plasmid, O: chromosome) Enterobacter spp. (B: plasmid) | 86 | T104A, N110D, E168Q, S171A, R214S |
2 | OXA-10-like | K. pneumoniae (B: plasmid) P. aeruginosa (B: chromosome, B: plasmid, O: chromosome) Enterobacter spp. (B: plasmid) A. baumannii (O: chromosome) | 42 | I10T, G20S, S27F, D55N, T107S, Y174F, E229G, S245N, E259A |
3 | OXA-9-like | K. pneumoniae (B: plasmid) P. aeruginosa (O: chromosome) Enterobacter spp. (B: plasmid) | 32 | Not found |
4 | OXA-2-like | Enterobacter spp. (B: chromosome) K. pneumoniae (B: plasmid) P. aeruginosa (B: chromosome, O: chromosome) | 12 | D321V |
5 | OXA-51-like | A. baumannii (B: chromosome, B: plasmid, O: chromosome) | 200 | A5T, T24S, E36V, E36D, E36K, A38G, A48V, Q57H, A96T, D105N, K107Q, K107E, D117, V129I, P130Q, K146N, L167V, K177Q, Q194P, K195E, D198H, L222W, D225N |
6 | OXA-20-like | A. baumannii (B: chromosome) | 1 | NA |
7 | OXA-23-like | A. baumannii (B: chromosome, B: plasmid, O: chromosome) P. aeruginosa (B: chromosome) | 156 | Not found |
8 | OXA-213-like | A. baumannii (B: chromosome) | 1 | NA |
9 | OXA-134-like | A. baumannii (B: chromosome, B: plasmid, O: chromosome) | 24 | D208G |
10 | OXA-58-like | A. baumannii (B: plasmid) | 14 | F114L, I161M, A256D |
11 | OXA-24-like | 11 | D224G | |
12 | OXA-1-like | K. pneumoniae (B: chromosome, B: plasmid, O: chromosome) P. aeruginosa (B: chromosome, B: plasmid, O: chromosome) Enterobacter spp. (B: chromosome, B: plasmid) | 154 | L28F, V64A, I102M, D103N, N2111E E223D, N268S |
13 | OXA-50-like | P. aeruginosa (B: chromosome, O: chromosome) | 189 | F6L, A8T, T17A, Q26R, R50C, R84K, D110E, R168H, K113E |
14 | OXA-33-like | P. aeruginosa (B: chromosome) | 2 | Not found |
15 | OXA-198-like | P. aeruginosa (O: chromosome) | 1 | NA |
16 | OXA-5-like | Enterobacter spp. (B: plasmid) P. aeruginosa (O: chromosome) | 4 | V117L |
OXA- 1-like | OXA- 2-like | OXA- 5-like | OXA- 9-like | OXA- 10-like | OXA- 20-like | OXA- 23-like | OXA- 24-like | OXA- 33-like | OXA- 48-like | OXA- 50-like | OXA- 51-like | OXA- 58-like | OXA- 134-like | OXA- 198-like | OXA- 213-like | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
OXA- 1-like | 100.00 | |||||||||||||||
OXA- 2-like | 26.00 | 100.00 | ||||||||||||||
OXA- 5-like | 27.50 | 32.30 | 100.00 | |||||||||||||
OXA- 9-like | 31.00 | 21.20 | 26.40 | 100.00 | ||||||||||||
OXA- 10-like | 27.10 | 34.00 | 80.90 | 26.30 | 100.00 | |||||||||||
OXA- 20-like | 26.90 | 72.70 | 35.60 | 21.70 | 33.90 | 100.00 | ||||||||||
OXA- 23-like | 24.10 | 27.00 | 33.90 | 19.90 | 33.20 | 28.80 | 100.00 | |||||||||
OXA- 24-like | 26.90 | 25.20 | 33.10 | 22.10 | 36.30 | 28.90 | 59.90 | 100.00 | ||||||||
OXA- 33-like | 100.00 | 26.00 | 27.60 | 31.00 | 27.10 | 26.90 | 24.10 | 26.90 | 100.00 | |||||||
OXA- 48-like | 27.20 | 39.20 | 44.10 | 22.50 | 45.40 | 40.90 | 35.60 | 31.80 | 27.20 | 100.00 | ||||||
OXA- 50-like | 25.00 | 32.90 | 35.80 | 25.60 | 33.30 | 35.80 | 40.90 | 36.20 | 25.00 | 36.10 | 100.00 | |||||
OXA- 51-like | 26.40 | 26.40 | 34.50 | 25.60 | 32.60 | 31.00 | 56.90 | 63.40 | 26.40 | 36.30 | 40.40 | 100.00 | ||||
OXA- 58-like | 21.80 | 28.40 | 35.40 | 25.30 | 36.00 | 29.60 | 47.70 | 48.60 | 21.80 | 34.00 | 39.40 | 48.30 | 100.00 | |||
OXA- 134-like | 25.00 | 28.70 | 34.50 | 23.70 | 35.20 | 28.50 | 55.90 | 55.90 | 25.00 | 32.10 | 38.10 | 54.50 | 52.70 | 100.00 | ||
OXA- 198-like | 26.40 | 34.80 | 30.70 | 22.50 | 31.30 | 36.30 | 27.20 | 31.00 | 26.40 | 35.30 | 33.00 | 28.40 | 32.50 | 32.60 | 100.00 | |
OXA- 213-like | 24.70 | 26.70 | 33.80 | 24.70 | 33.00 | 30.00 | 56.50 | 62.00 | 24.70 | 36.60 | 39.60 | 97.10 | 47.20 | 53.00 | 28.10 | 100.00 |
Super-Imposition | OXA-1-like | OXA-2-like | OXA-5-like | OXA-9-like | OXA-10-like | OXA-20-like | OXA-23-like | OXA-24-like | OXA-33-like | OXA-48-like | OXA-50-like | OXA-51-like | OXA-58-like | OXA-134-like | OXA-198-like | OXA-213-like |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
OXA-1-like | 0 | |||||||||||||||
OXA-2-like | 0.972 | 0 | ||||||||||||||
OXA-5-like | 1.112 | 0.704 | 0 | |||||||||||||
OXA-9-like | 0.784 | 1.099 | 1.756 | 0 | ||||||||||||
OXA-10-like | 1.058 | 0.762 | 0.268 | 1.738 | 0 | |||||||||||
OXA-20-like | 0.96 | 0.226 | 0.715 | 1.174 | 0.759 | 0 | ||||||||||
OXA-23-like | 1.143 | 0.902 | 1.108 | 1.768 | 1.118 | 0.898 | 0 | |||||||||
OXA-24-like | 1.023 | 1.007 | 1.027 | 1.052 | 1.07 | 0.946 | 0.426 | 0 | ||||||||
OXA-33-like | 0 | 0.972 | 1.112 | 0.784 | 1.058 | 0.96 | 1.143 | 1.023 | 0 | |||||||
OXA-48-like | 0.817 | 0.613 | 0.659 | 0.946 | 0.805 | 0.645 | 0.823 | 0.848 | 0.817 | 0 | ||||||
OXA-50-like | 0.811 | 0.623 | 0.51 | 0.699 | 0.637 | 0.636 | 0.798 | 0.798 | 0.811 | 0.375 | 0 | |||||
OXA-51-like | 0.963 | 0.893 | 1.081 | 1.364 | 1.131 | 0.912 | 0.41 | 0.478 | 0.963 | 0.817 | 0.759 | 0 | ||||
OXA-58-like | 0.987 | 1.007 | 0.848 | 2.324 | 0.881 | 1.054 | 0.623 | 0.639 | 0.987 | 0.926 | 0.882 | 0.616 | 0 | |||
OXA-134-like | 1.143 | 0.902 | 1.108 | 1.768 | 1.118 | 0.898 | 0 | 0.426 | 1.143 | 0.823 | 0.798 | 0.41 | 0.623 | 0 | ||
OXA-198-like | 0.78 | 0.581 | 0.548 | 2.466 | 0.705 | 0.556 | 0.727 | 0.784 | 0.78 | 0.381 | 0.277 | 0.701 | 0.915 | 0.727 | 0 | |
OXA-213-like | 0.963 | 0.893 | 1.081 | 1.364 | 1.131 | 0.912 | 0.41 | 0.478 | 0.963 | 0.817 | 0.759 | 0 | 0.616 | 0.41 | 0.701 | 0 |
S. No. | Protein Name | PDB ID | Query Coverage (%) | Identity (%) |
---|---|---|---|---|
1 | OXA-10-like | 1K6R | 92 | 100 |
2 | OXA-2-like | 1K38 | 92 | 99.60 |
3 | OXA-48-like | 5OE0 | 100 | 99.60 |
4 | OXA-24-like | 4WM9 | 89 | 99.50 |
5 | OXA-58-like | 4OH0 | 100 | 99.29 |
6 | OXA-1-like | 1M6K | 90 | 98.8 |
7 | OXA-213-like | 4ZDX | 100 | 97 |
8 | OXA-33-like | 1M6K | 90 | 98.80 |
9 | OXA-51-like | 4ZDX | 100 | 97 |
10 | OXA-23-like | 4JF4 | 89 | 100 |
11 | OXA-5-like | 1FOF | 91 | 84.01 |
12 | OXA-20-like | 6XJ3 | 92 | 77.30 |
13 | OXA-134-like | 4JF4 | 85 | 63.90 |
14 | OXA-9-like | 6NHU | 89 | 46.06 |
15 | OXA-198-like | 6NLW | 88 | 40.60 |
16 | OXA-50-like | 4JF4 | 90 | 44.30 |
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Pandey, D.; Singhal, N.; Kumar, M. Investigating the OXA Variants of ESKAPE Pathogens. Antibiotics 2021, 10, 1539. https://doi.org/10.3390/antibiotics10121539
Pandey D, Singhal N, Kumar M. Investigating the OXA Variants of ESKAPE Pathogens. Antibiotics. 2021; 10(12):1539. https://doi.org/10.3390/antibiotics10121539
Chicago/Turabian StylePandey, Deeksha, Neelja Singhal, and Manish Kumar. 2021. "Investigating the OXA Variants of ESKAPE Pathogens" Antibiotics 10, no. 12: 1539. https://doi.org/10.3390/antibiotics10121539
APA StylePandey, D., Singhal, N., & Kumar, M. (2021). Investigating the OXA Variants of ESKAPE Pathogens. Antibiotics, 10(12), 1539. https://doi.org/10.3390/antibiotics10121539