Comparative Genomics of Clinical and Environmental Isolates of Vibrio spp. of Colombia: Implications of Traits Associated with Virulence and Resistance
Abstract
:1. Introduction
2. Results
2.1. Characteristics of the Assembled Genomes of Vibrio spp.
2.2. Vibrio parahaemolyticus
2.3. Vibrio vulnificus
2.4. Vibrio alginolyticus
2.5. Vibrio diabolicus
2.6. Vibrio fluvialis
2.7. Vibrio furnissii
3. Discussion
4. Materials and Methods
4.1. Study Area and Sampling
4.2. Whole Genome Sequencing, De Novo Assembly and Annotation
4.3. Characterization of the Most Important Species in Public Health
4.4. Pangenome and Phylogenomic Analyses
4.5. Identification of Virulence Factors and Antimicrobial Resistance Determinants
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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COG20_Category | Enrichment_Score | Unadjusted_p_Value | Adjusted_q_Value | Associated_Isolate_Sources |
---|---|---|---|---|
Cell motility|Intracellular trafficking, secretion and vesicular transport | 17 | 3.74 × 10−5 | 3.03 × 10−3 | clinical |
Cell cycle control, cell division, chromosome partitioning|Cell motility | 13.388 | 2.53 × 10−4 | 3.16 × 10−3 | environmental |
Amino acid transport and metabolism|Nucleotide transport and metabolism | 13.246 | 2.73 × 10−4 | 3.16 × 10−3 | clinical |
Cell cycle control, cell division, chromosome partitioning|Coenzyme transport and metabolism | 13.246 | 2.73 × 10−4 | 3.16 × 10−3 | clinical |
Nucleotide transport and metabolism|Signal transduction mechanisms | 13.246 | 2.73 × 10−4 | 3.16 × 10−3 | clinical |
Signal transduction mechanisms|Signal transduction mechanisms | 13.246 | 2.73 × 10−4 | 3.16 × 10−3 | clinical |
Carbohydrate transport and metabolism|Transcription | 13.246 | 2.73 × 10−4 | 3.16 × 10−3 | environmental |
Cell cycle control, cell division, chromosome partitioning | 10.578 | 1.14 × 10−3 | 1.03 × 10−2 | clinical |
Signal transduction mechanisms|Intracellular trafficking, secretion and vesicular transport | 10.578 | 1.14 × 10−3 | 1.03 × 10−2 | clinical |
Intracellular trafficking, secretion and vesicular transport|General function prediction only|Transcription | 9.745 | 1.80 × 10−3 | 1.03 × 10−2 | clinical |
Nucleotide transport and metabolism | 9.745 | 1.80 × 10−3 | 1.03 × 10−2 | environmental |
Species | Isolate | Type | GC (%) | Size (kbp) | Predicted Virulence Genes (Min e-Value 0.01) |
---|---|---|---|---|---|
V. parahaemolyticus | PV1 | Putative ICE | 44.45 | 195 | VP1611(MAM7), mshE, mshH, mshA, mshL, mshG, mshJ, tcpI |
V. parahaemolyticus | PV173 | Putative IME | 39.38 | 82 | vcrD2, vscC2, vopL, vscN2, vopB2, vscU2, VPA1351, vopA/vopP, VPA1353, vopZ, vopD2, vopT, vscR2, vscT2, VPA1350, vscJ2, VPA1352, VPA1331, VPA1331, VPA1363, VPA1337, VPA1340, vscS2, vscQ2, acfD, tdh, flhA, yscV/lcrD, flhA, vcrD, yscN, mxiA, flhA |
V. parahaemolyticus | PV278 | Putative IME | 40.6 | 35 | |
V. fluvialis | PV3 | Putative ICE with T4SS | 52 | 166 | IlpA, motB, motA |
V. fluvialis | PV4 | Putative IME | 46.86 | 74 | |
V. fluvialis | PV9 | Putative IME | 50.94 | 40 | |
V. fluvialis | PV50 | Putative ICE with T4SS | 48.48 | 233 | tcpI |
V. fluvialis | PV50 | Putative IME | 45.8 | 77 | |
V. fluvialis | PV59 | Putative ICE with T4SS | 47.8 | 215 | cqsA |
V. fluvialis | PV59 | Putative ICE with T4SS | 48.85 | 231 | |
V. fluvialis | PV60 | Putative ICE with T4SS | 48.4 | 296 | flaC,flaB,flgA,flgJ, flaD, flgT, flgP, flgI, flgL,flgC,flgO,flgF,flgB,cheR,cheV,flgK,flgD,flaA,flgH,flgG,tcpI,flgN |
V. fluvialis | PV76 | Putative ICE with T4SS | 47.74 | 226 | cqsA |
V. fluvialis | PV92 | Putative IME with T4SS | 47.99 | 183 | cqsA |
V. fluvialis | PV92 | Putative IME | 50.62 | 48 | |
V. fluvialis | PV105 | Putative ICE with T4SS | 49.15 | 165 | flgD |
V. fluvialis | PV131 | Putative IME | 47.34 | 52 | |
V. alginolyticus | PV126 | Putative IME | 41.8 | 75 | |
V. alginolyticus | PV242 | Putative IME | 45.81 | 15 | |
V. vulnificus | PV35 | Putative IME | 43.19 | 79 | |
V. vulnificus | PV159 | Putative IME | 40.53 | 15 | |
V. vulnificus | PV194 | Putative IME | 49.13 | 62 | |
V. vulnificus | PV207 | Putative IME | 40.18 | 57 | |
V. furnissii | PV10 | Putative ICE with T4SS | 53.14 | 173 | |
V. furnissii | PV88 | Putative IME | 45.96 | 80 | |
V. furnissii | PV169_L | Putative ICE with T4SS | 51.94 | 388 |
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Pérez-Duque, A.; Gonzalez-Muñoz, A.; Arboleda-Valencia, J.; Vivas-Aguas, L.J.; Córdoba-Meza, T.; Rodriguez-Rey, G.T.; Díaz-Guevara, P.; Martinez-Urtaza, J.; Wiesner-Reyes, M. Comparative Genomics of Clinical and Environmental Isolates of Vibrio spp. of Colombia: Implications of Traits Associated with Virulence and Resistance. Pathogens 2021, 10, 1605. https://doi.org/10.3390/pathogens10121605
Pérez-Duque A, Gonzalez-Muñoz A, Arboleda-Valencia J, Vivas-Aguas LJ, Córdoba-Meza T, Rodriguez-Rey GT, Díaz-Guevara P, Martinez-Urtaza J, Wiesner-Reyes M. Comparative Genomics of Clinical and Environmental Isolates of Vibrio spp. of Colombia: Implications of Traits Associated with Virulence and Resistance. Pathogens. 2021; 10(12):1605. https://doi.org/10.3390/pathogens10121605
Chicago/Turabian StylePérez-Duque, Alejandra, Andrea Gonzalez-Muñoz, Jorge Arboleda-Valencia, Lizbeth Janet Vivas-Aguas, Tania Córdoba-Meza, Ghennie Tatiana Rodriguez-Rey, Paula Díaz-Guevara, Jaime Martinez-Urtaza, and Magdalena Wiesner-Reyes. 2021. "Comparative Genomics of Clinical and Environmental Isolates of Vibrio spp. of Colombia: Implications of Traits Associated with Virulence and Resistance" Pathogens 10, no. 12: 1605. https://doi.org/10.3390/pathogens10121605
APA StylePérez-Duque, A., Gonzalez-Muñoz, A., Arboleda-Valencia, J., Vivas-Aguas, L. J., Córdoba-Meza, T., Rodriguez-Rey, G. T., Díaz-Guevara, P., Martinez-Urtaza, J., & Wiesner-Reyes, M. (2021). Comparative Genomics of Clinical and Environmental Isolates of Vibrio spp. of Colombia: Implications of Traits Associated with Virulence and Resistance. Pathogens, 10(12), 1605. https://doi.org/10.3390/pathogens10121605