Survival and Genome Diversity of Vibrio parahaemolyticus Isolated from Edible Aquatic Animals
Abstract
:1. Introduction
2. Materials and Methods
2.1. V. parahaemolyticus Isolates and Culture Conditions
2.2. Genomic DNA Preparation
2.3. PCR Assay
2.4. Genome Sequencing, Assembly, and Annotation
2.5. Prediction of MGEs
2.6. Comparative Genome Analysis
3. Results
3.1. Genotypes and Phenotypes of the Six V. parahaemolyticus Isolates
3.2. Survival of the Six V. parahaemolyticus Isolates at Different pH and NaCl Conditions
3.3. Genome Features of the Six V. parahaemolyticus Isolates Originating in Edible Aquatic Animals
3.4. Phylogenetic Relatedness of the Six V. parahaemolyticus Isolates Originating in Edible Aquatic Animals
3.5. Diverse MGEs in the Six V. parahaemolyticus Genomes of Edible Aquatic Animal Origins
3.5.1. GIs
3.5.2. Prophages
3.5.3. Integrons
3.5.4. ISs
3.5.5. ICEs
3.6. CRISPR-Cas Systems
3.7. Putative Virulence-Associated Genes in the Six V. Parahaemolyticus Genomes
3.8. Antibiotic Resistance-Associated Genes in the Six V. parahaemolyticus Genomes
3.9. Heavy Metal Tolerance-Associated Genes in the Six V. parahaemolyticus Genomes
3.10. Strain-Specific Genes of the Six V. parahaemolyticus Isolates of Edible Aquatic Animal Origins
4. Discussion
5. 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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Genome Feature | V. parahaemolyticus Isolate | |||||
---|---|---|---|---|---|---|
L7-7 | N1-22 | N3-33 | N4-46 | N8-42 | Q8-15 | |
Genome size (bp) | 4,937,042 | 5,067,778 | 5,018,989 | 5,049,514 | 5,010,476 | 4,993,599 |
G + C (%) | 45.36 | 45.20 | 45.32 | 45.29 | 45.39 | 45.34 |
DNA Scaffold | 54 | 58 | 60 | 77 | 61 | 36 |
Total predicted gene | 4749 | 4919 | 4815 | 4878 | 4832 | 4756 |
Protein-coding gene | 4624 | 4791 | 4707 | 4768 | 4706 | 4622 |
RNA gene | 125 | 128 | 108 | 110 | 126 | 134 |
Genes assigned to COG | 3862 | 3892 | 3852 | 3886 | 3875 | 3854 |
Genes with unknown function | 1064 | 1094 | 1086 | 1107 | 1102 | 1093 |
GI | 6 | 9 | 6 | 6 | 7 | 5 |
Prophage gene cluster | 0 | 1 | 0 | 1 | 2 | 1 |
CRISPR-Cas | 0 | 2 | 3 | 0 | 0 | 1 |
Integron | 2 | 1 | 5 | 11 | 8 | 6 |
IS | 3 | 0 | 1 | 0 | 1 | 1 |
16S rDNA sequence accession no. | MW386441 | MW386442 | MW386445 | MW386446 | MW386450 | MW386453 |
Antimicrobial Agent | Gene | V. parahaemolyticus Isolates |
---|---|---|
Cephalosporin | acrB | L7-7, N1-22, N3-33, N4-46, N8-42, Q8-15 |
Phenicol | catB | L7-7, N1-22, N3-33, N4-46, N8-42, Q8-15 |
SoxR | L7-7, N1-22, N3-33, N4-46, N8-42, Q8-15 | |
Fluoroquinolone | hns | L7-7, N1-22, N3-33, N4-46, N8-42, Q8-15 |
acrB | L7-7, N1-22, N3-33, N4-46, N8-42, Q8-15 | |
qnr | L7-7, N1-22, N3-33, N4-46, N8-42, Q8-15 | |
crp | L7-7, N1-22, N3-33, N4-46, N8-42, Q8-15 | |
Tetracycline | tet(35) | L7-7, N1-22, N3-33, N4-46, N8-42, Q8-15 |
tet(34) | L7-7, N1-22, N3-33, N4-46, N8-42, Q8-15 | |
hns | L7-7, N1-22, N3-33, N4-46, N8-42, Q8-15 | |
acrB | L7-7, N1-22, N3-33, N4-46, N8-42, Q8-15 | |
SoxR | L7-7, N1-22, N3-33, N4-46, N8-42, Q8-15 | |
Beta-lactam | blaCARB-18 | N3-33 |
blaCARB-19 | L7-7, N1-22, N8-42, Q8-15 | |
blaCARB-21 | L7-7, N1-22, N3-33, N8-42, Q8-15 | |
blaCARB-23 | N4-46 | |
blaCARB-29 | N3-33, N4-46,Q8-15 | |
blaCARB-35 | N1-22 | |
blaCARB-33 | N3-33 | |
blaCARB-41 | N3-33 | |
blaCARB-44 | L7-7, N8-42 | |
blaCARB-45 | N1-22 | |
blaCARB-48 | N1-22 | |
Diaminopyrimidine | folA | L7-7, N1-22, N3-33, N4-46, N8-42, Q8-15 |
Macrolide | macB | L7-7, N1-22, N3-33, N4-46, N8-42, Q8-15 |
Nitroimidazole | msbA | L7-7, N1-22, N3-33, N4-46, N8-42, Q8-15 |
Heavy metal | cusA | L7-7, N1-22, N3-33, N4-46, N8-42, Q8-15 |
Heavy metal | cusR | L7-7, N1-22, N3-33, N4-46, N8-42, Q8-15 |
Heavy metal | cusS | L7-7, N1-22, N3-33, N4-46, N8-42, Q8-15 |
Heavy metal | zntA | L7-7, N1-22, N3-33, N4-46, N8-42, Q8-15 |
Heavy metal | copA | L7-7, Q8-15 |
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Xu, D.; Peng, X.; Xie, L.; Chen, L. Survival and Genome Diversity of Vibrio parahaemolyticus Isolated from Edible Aquatic Animals. Diversity 2022, 14, 350. https://doi.org/10.3390/d14050350
Xu D, Peng X, Xie L, Chen L. Survival and Genome Diversity of Vibrio parahaemolyticus Isolated from Edible Aquatic Animals. Diversity. 2022; 14(5):350. https://doi.org/10.3390/d14050350
Chicago/Turabian StyleXu, Dingxiang, Xu Peng, Lu Xie, and Lanming Chen. 2022. "Survival and Genome Diversity of Vibrio parahaemolyticus Isolated from Edible Aquatic Animals" Diversity 14, no. 5: 350. https://doi.org/10.3390/d14050350