First Record of the Rare Species Aeromonas lusitana from Rainbow Trout (Oncorhynchus mykiss, Walbaum): Comparative Analysis with the Existing Strains
Abstract
:1. Introduction
2. Materials and Methods
2.1. Bacterial Strains
2.2. Phenotypic Characterization and Antimicrobial Susceptibility Testing
2.3. Fingerprinting by ERIC-PCR
2.4. Putative Virulence Genes Detection
2.5. Genome Sequencing, Assembling and Annotation
2.6. Phylogenetic Analysis Based on the Genome
2.7. Genome Information and Comparative Analysis
2.8. Genomic Indexes
2.9. Pangenome and Core Genes Analysis
2.10. Comparison of Predicted Protein Sequences
2.11. Protein Count and Distribution in Subsystems
2.12. Citrate Synthase Sequence Analysis in A. lusitana
3. Results and Discussion
3.1. Fingerprinting by ERIC-PCR
3.2. Phenotypic Characterization and Antimicrobial Susceptibility Testing
3.3. Putative Virulence Genes Detection
3.4. Phylogenetic Analysis with 7 Housekeeping Genes Extracted from the Genomes
3.5. Comparison of ANI and isDDH Values Obtained between A. lusitana and Its Closest Species
3.6. Genomic Information and Its Comparison to Other Related and Non-Related Species
3.7. Pangenome and Accessory Genome Analysis
3.8. Comparison of Predicted Protein Sequences
3.9. Protein Count and Distribution in Subsystems
3.10. Citrate Synthase Sequence Analysis in A. lusitana
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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ESV-351 | CECT 7828T | Isolates (4) | |
---|---|---|---|
β-hemolysis | + | + | + |
Indole | + b | - | - |
MR | + | + | + |
LDC | + | + | + |
Glucose (gas) | + | + | + |
Citrate | + | + | + |
Hydrolysis of: | |||
SDS | - | - | V |
Aesculin | + | + | + |
Starch | + | + | + |
Elastase | ND | + | + |
Acid from: | |||
Glycerol | + | + | + |
L-arabinose | - | - | - |
Salicin | + | + | + |
Utilization of: | |||
DL-lactate | - | - | - |
L-arabinose | - | - | - |
Growth at: 4.5% NaCl | + | + | + |
Antimicrobial Agent (μg) a | Results (MIC) | Breakpoints | |||
---|---|---|---|---|---|
ESV-351 | CECT 7828T | S | I | R | |
Amikacin (30 μg) | S (≤8) | S (≤8) | ≤16 | 32 | ≥64 |
Ampicillin (10 μg) | I (>16) | I (>16) | ≤8 | 16 | ≥32 |
Amoxicillin-clavulanic acid (20/10 μg) | I (>16/8) | I (>16/8) | ≤8/4 | 16/8 | ≥32/16 |
Aztreonam (30 μg) | S (≤1) | S (≤1) | ≤8 | 16 | ≥32 |
Ceftazidime (30 μg) | S (≤1) | S (≤1) | ≤8 | 16 | ≥32 |
Ceftriaxone (30 μg) | S (33) b | S (33) b | ≥21 | 14–20 | ≤13 |
Cephalothin (30 μg) | I (>16) | I (>16) | ≤8 | 16 | ≥32 |
Ciprofloxacin (30 μg) | S (42) b | S (42) b | ≥21 | 16–20 | ≤15 |
Cefotaxime (30 μg) | S (≤1) | S (≤1) | ≤8 | 16–32 | ≥64 |
Cefoxitin (30 μg) | S (≤8) | S (≤8) | ≤8 | 16 | ≥32 |
Ciprofloxacin (5 μg) | S (≤0.5) | S (≤0.5) | ≤1 | 2 | ≥4 |
Cefepime (30 μg) | S (≤1) | S (≤1) | ≤8 | 16 | ≥32 |
Cefuroxime (30 μg) | S (8) b | S (8) b | ≤8 | 16 | ≥32 |
Ertapenem (10 μg) | S (≤0.5) | S (≤0.5) | ≤2 | 4 | ≥8 |
Gentamicin (10 μg) | S (≤2) | S (≤2) | ≤4 | 8 | ≥16 |
Imipenem (10 μg) | S (≤1) | S (≤1) | ≤4 | 8 | ≥16 |
Nalidixic acid (30 μg) | S (≤16) | S (≤16) | ≤8 | 16 | ≥16 |
Piperacillin (100 μg) | S (29) b | S (29) b | ≥21 | 18–20 | ≤17 |
Piperacillin-tazobactam (100/10 μg) | S (≤8) | S (≤8) | ≤16/4 | 32/4–64/4 | ≥128/4 |
Tetracycline (30 μg) | S (27) b | S (27) b | ≥19 | 15–18 | ≤14 |
Trimethoprim-sulfamethoxazole (25 μg) | S (≤2/38) | S (≤2/38) | ≤2/38 | - | ≥4/76 |
Tigecycline (15 μg) | S (≤1) | S (≤1) | ≤1 | 2 | ≥2 |
Tobramycin (10 μg) | S (≤2) | S (≤2) | ≤2 | 4 | ≥4 |
Strain | Source | laf | act | ast | alt | aerA | Lipase Genes | Serine Protease Genes | ascF-G | ascV | aexT | stx1 | stx2 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ESV-351 | Gills of rainbow trout | - | + | - | - | + | + | + | - | - | - | - | - |
CECT 7828T | Untreated water | + | - | - | - | + | + | + | + | + | + | - | - |
A.136/15 | Untreated water | + | - | - | - | + | + | + | + | + | - | - | - |
L8-3 | Vegetables | + | - | - | - | + | + | - | + | + | - | - | - |
L10-4 | Vegetables | + | + | - | - | + | + | + | - | - | - | - | - |
A.2876 | Untreated water | - | + | - | - | + | + | + | - | - | - | - | - |
Species | Size (Mb) | Average | Protein Coding Genes | Average | tRNAs | Average | G+C (%) | Average |
---|---|---|---|---|---|---|---|---|
A. lusitana ESV-351 A. lusitana CECT 7828T | 4.74 4.55 | 4.64 | 4251 4069 | 4160 | 110 98 | 104 | 60.7 61.0 | 60.8 |
Closest species | ||||||||
A. tecta CECT 7028T A. eucrenophila CECT 4224T A. aquatica CECT 8025T A. encheleia CECT 4342T | 4.75 4.54 4.58 4.47 | 4.56 | 4267 4098 4091 4051 | 4094 | 96 101 82 94 | 95 | 60.1 61.2 61.2 62.0 | 61.2 |
Closed genomes available at Genbank | ||||||||
A. salmonicida A449 A. hydrophila ATCC 7966T A. caviae Ae398 A. veronii B565 A. salmonicida 01-B526 A. dhakensis AAK1 | 4.70 4.74 4.43 4.55 4.75 4.81 | 4.72 | 4388 4128 3690 4057 4179 4214 | 4153 | 110 128 ND 102 111 ND | 110 | 58.5 61.5 61.4 58.7 58.5 61.8 | 60.0 |
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Fernández-Bravo, A.; Vega-Sánchez, V.; Pérez-Cataluña, A.; Latif-Eugenín, F.; Beaz-Hidalgo, R.; Martínez-Murcia, A.; Soriano-Vargas, E.; Cabrero-Martínez, O.A.; Castro-Escarpulli, G.; Figueras, M.J. First Record of the Rare Species Aeromonas lusitana from Rainbow Trout (Oncorhynchus mykiss, Walbaum): Comparative Analysis with the Existing Strains. Pathogens 2022, 11, 1299. https://doi.org/10.3390/pathogens11111299
Fernández-Bravo A, Vega-Sánchez V, Pérez-Cataluña A, Latif-Eugenín F, Beaz-Hidalgo R, Martínez-Murcia A, Soriano-Vargas E, Cabrero-Martínez OA, Castro-Escarpulli G, Figueras MJ. First Record of the Rare Species Aeromonas lusitana from Rainbow Trout (Oncorhynchus mykiss, Walbaum): Comparative Analysis with the Existing Strains. Pathogens. 2022; 11(11):1299. https://doi.org/10.3390/pathogens11111299
Chicago/Turabian StyleFernández-Bravo, Ana, Vicente Vega-Sánchez, Alba Pérez-Cataluña, Fadua Latif-Eugenín, Roxana Beaz-Hidalgo, Antonio Martínez-Murcia, Edgardo Soriano-Vargas, Omar Alejandro Cabrero-Martínez, Graciela Castro-Escarpulli, and Maria José Figueras. 2022. "First Record of the Rare Species Aeromonas lusitana from Rainbow Trout (Oncorhynchus mykiss, Walbaum): Comparative Analysis with the Existing Strains" Pathogens 11, no. 11: 1299. https://doi.org/10.3390/pathogens11111299