Genomic Virulence Features of Two Novel Species Nocardia barduliensis sp. nov. and Nocardia gipuzkoensis sp. nov., Isolated from Patients with Chronic Pulmonary Diseases
Abstract
:1. Introduction
2. Case Reports
2.1. Case 1
2.2. Case 2
3. Materials and Methods
3.1. Isolation and Phenotypic Characterization
3.2. Whole Genome Sequencing
3.3. Identification and Phylogenetic Studies
3.4. Virulence Factors
- Pathogen species: Mycobacterium tuberculosis
- Disease: tuberculosis
- Host species: Homo sapiens (related to human) and Mus musculus (house mouse)
- Experimental technique: partial and full gene deletions, complementation and disruption.
- Mutant phenotype: increased virulence (hypervirulence); loss of pathogenicity; reduced virulence.
3.5. Antimicrobial Gene Resistance and Toxic Compound Tolerance
3.6. Comparative Genomic of VF-Associated Genes
4. Results and Discussion
4.1. Phenotypic Characterization
4.2. Molecular Characterization and Genome-Based Taxonomy
4.3. Virulence Factors
4.4. Comparative Genomic of VF-Encoding Genes
4.5. Estimation of Being Human Pathogen
4.6. Antimicrobial Gene Resistance and Toxic Compound Tolerance
4.7. Description of Nocardia barduliensis sp. nov.
4.8. Description of Nocardia gipuzkoensis sp. nov.
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Characteristics | Isolate 335427T | N. asiatica DSM 44668T | Isolate 234509T | N. abscessus DSM 44432T |
---|---|---|---|---|
Carbon source utilization | ||||
β-Gentiobiose and L-Fucose | + | + | - | - |
β-Methyl-D-Glucoside | + | w | w | + |
Dextrin | - | + | - | + |
D-Arabitol | w | + | - | - |
D-Cellobiose | - | - | - | w |
D-Fructose, D-Fructose-6-Phosphate, N-Acetyl-β-D-Mannosamine and L-Rhamnose | + | + | - | + |
D-Fucose; D-Galactose, D-Mannose, Inosine, myo-Inositol, 3-O-Methyl-D-Glucose and N-Acetyl-D-Galactosamine | + | - | - | - |
D-Galacturonic Acid and Glucuronamide | - | w | - | - |
D-Glucose and Turanose | w | + | + | + |
D-Glucose-6-Phosphate | + | - | + | + |
D-Maltose | w | - | + | + |
D-Melibiose | w | + | - | + |
D-Saccharic Acid and N-Acetyl-D-Glucosamine | + | w | + | + |
D-Salicin | w | w | + | + |
D-Trehalose | - | - | + | w |
Gelatin | - | + | - | - |
N-Acetyl-Neuraminic Acid | + | w | - | - |
Pectin | + | w | - | w |
Aminoacids | ||||
L-Histidine | + | + | - | + |
L-Serine | w | - | - | + |
Organic acids | ||||
Acetoacetic Acid | + | w | + | + |
α-Hydroxy-Butyric Acid | + | + | - | + |
α-Keto-Butyric Acid | + | - | - | + |
Bromo-Succinic Acid | - | - | + | + |
Butyric Acid | w | - | w | + |
D-Gluconic Acid | w | + | - | - |
D-Glucuronic Acid | + | w | + | - |
D-Lactic Acid Methyl Ester | + | - | w | - |
D-Malic Acid | + | + | + | w |
L-Lactic Acid | + | + | w | - |
Mucic Acid | + | + | - | - |
Methyl Pyruvate | w | - | + | + |
p-Hydroxy-Phenylacetic Acid | - | - | - | + |
Inhibitory compounds | ||||
Lithium Chloride | - | - | - | w |
Sodium Bromate | - | - | - | + |
Tetrazolium Violet | w | - | + | - |
Vancomycin | - | - | - | + |
1% Sodium Lactate | w | - | + | + |
Gene Identity (%) | |||||||
---|---|---|---|---|---|---|---|
Isolate | Hit Taxon | 16S rRNA | hsp65 | secA | gyrB | rpoB | dDDH |
335427T | |||||||
Isolate 234509T | 99.0 | 98.7 | 97.1 | 92.9 | 99.8 | 44.2 | |
N. asiatica | 99.5 | 98.1 | 98.5 | 94.4 | 99.7 | 53.5 | |
N. arthritidis | 99.0 | 96.2 | 97.0 | 92.8 | 96.0 | 36.6 | |
N. abscessus | 98.9 | 97.5 | 97.9 | 93.1 | 99.4 | 44.6 | |
N. farcinica | 98.8 | 92.9 | 88.5 | 91.9 | 97.2 | 23.3 | |
N. kroppenstedtii | 98.7 | - | - | - | - | N/A | |
N. araoensis | 98.6 | 98.3 | 97.0 | 98.5 | 35.7 | ||
N. beijingensis | 98.4 | 97.9 | 97.6 | 93.5 | 98.2 | 35.0 | |
234509T | |||||||
Isolate 335427T | 99.0 | 98.7 | 97.1 | 92.9 | 99.8 | 44.2 | |
N. abscessus | 100.0 | 98.5 | 98.5 | 99.8 | 99.4 | 67.9 | |
N. asiatica | 99.0 | 98.3 | 98.2 | 97.9 | 99.2 | 43.0 | |
N. exalbida | 99.0 | 98.8 | 96.4 | 97.9 | 99.0 | 37.6 | |
N. cyriacigeorgica | 98.9 | 96.3 | 87.9 | 93.3 | 97.5 | 22.9 | |
N. shimofusensis | 98.9 | 96.8 | 85.9 | 92.8 | 97.6 | 22.5 | |
N. asteroides | 98.7 | 95.5 | 98.5 | 92.7 | 92.7 | 22.1 | |
N. arthritidis | 98.5 | 98.5 | 96.5 | 91.9 | 99.1 | 37.6 | |
N. neocaledoniensis | 98.3 | 95.9 | 86.5 | 92.6 | 96.4 | 22.1 |
Antibiotic | Susceptibility Criteria 1 | Isolate 234509T | Isolate 335427T |
---|---|---|---|
Penicillin 2 | ND | 0.25 | 0.25 |
Amoxicillin 2 | ND | 0.38 | 0.75 |
Amoxicillin-clavulanic acid | ≤8/4 | <2/1 | 16/8 |
Ceftriaxone | ≤8 | <4 | <4 |
Cefepime | ≤8 | <1 | 2 |
Imipenem | ≤4 | <2 | <2 |
Clarithromycin | ≤2 | 2 | 4 |
Doxycycline | ≤1 | <0.12 | <0.12 |
Minocycline | ≤1 | <1 | <1 |
Trimethoprim/sulfamethoxazole | ≤2/38 | <0.25/4.75 | <0.25/4.75 |
Ciprofloxacin | ≤1 | >4 | 1 |
Levofloxacin | ≤1 | 4 | 0.5 |
Tobramycin | ≤4 | <1 | <1 |
Amikacin | ≤8 | <1 | <1 |
Tigecycline | ND | 0.06 | 0.25 |
Linezolid | ≤8 | <1 | <1 |
Isolate | Gene | AMR Gene Family | Drug Class | Resistance Mechanism | Identity of Matching Region (%) |
---|---|---|---|---|---|
335427T | |||||
c | small multidrug resistance (SMR) antibiotic efflux pump | aminoglycoside antibiotic, tetracycline antibiotic, phenicol antibiotic | antibiotic efflux | 100 | |
tet44 | tetracycline-resistant ribosomal protection protein | tetracycline | target protection | ||
lpe | resistance-nodulation-cell division (RND) antibiotic efflux pump | - | efflux | 100 | |
vanHM | glycopeptide antibiotic | - | target alteration | 100 | |
234509T | |||||
- | EmrB/QacA subfamily drug resistance transporter | - | 85.9 | ||
- | MurA regulator CwlM implicated in cell wall metabolism and antibiotic tolerance | - | 99.2 |
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Nouioui, I.; Cortés-Albayay, C.; Neumann-Schaal, M.; Vicente, D.; Cilla, G.; Klenk, H.-P.; Marimón, J.M.; Ercibengoa, M. Genomic Virulence Features of Two Novel Species Nocardia barduliensis sp. nov. and Nocardia gipuzkoensis sp. nov., Isolated from Patients with Chronic Pulmonary Diseases. Microorganisms 2020, 8, 1517. https://doi.org/10.3390/microorganisms8101517
Nouioui I, Cortés-Albayay C, Neumann-Schaal M, Vicente D, Cilla G, Klenk H-P, Marimón JM, Ercibengoa M. Genomic Virulence Features of Two Novel Species Nocardia barduliensis sp. nov. and Nocardia gipuzkoensis sp. nov., Isolated from Patients with Chronic Pulmonary Diseases. Microorganisms. 2020; 8(10):1517. https://doi.org/10.3390/microorganisms8101517
Chicago/Turabian StyleNouioui, Imen, Carlos Cortés-Albayay, Meina Neumann-Schaal, Diego Vicente, Gustavo Cilla, Hans-Peter Klenk, Jose María Marimón, and Maria Ercibengoa. 2020. "Genomic Virulence Features of Two Novel Species Nocardia barduliensis sp. nov. and Nocardia gipuzkoensis sp. nov., Isolated from Patients with Chronic Pulmonary Diseases" Microorganisms 8, no. 10: 1517. https://doi.org/10.3390/microorganisms8101517