Characterization of CRISPR genetic sequences in microorganisms associated with infections in shrimp (Litopenaeus vannamei)

Abstract

In shrimp farming, the family of proteobacteria Vibrionaceae, especially the species of the genus Vibrio, represent one of the main responsible for infections in shrimp production (Litopenaeus vannamei), generating great losses to this industry. Phagotherapy emerges as a novel alternative for the control of said infections in substitution to the use of antibiotics, thanks to the specific inhibitory activity of these viruses. However, it is necessary to take into account the presence in prokaryotes of genetic sequences called clusters of regularly interspaced short palindromic repeats (CRISPR) that act as an immune system against invasion of external mobile genetic elements such as phage or plasmids. Due to its characteristics, the CRISPR/Cas system is used as a tool for gene editing. This study presents the comparative analysis of 7 CRISPR loci found in 5 sequences of complete genomes, available in the database of NCBI/GenBank, to determine the potential use of the phage strategy in shrimp farming. The CRISPR systems corresponded to types I-E, I-F and III-D. 53 % of the spacers (75/142) presented homology with plasmids, while the remaining 47 % (67/142) showed homology with bacteriophages, mostly non-typical Vibrio infective viruses. The use of phage therapy is proposed as a treatment for infections caused by members of the family Vibrionaceae in shrimp cultures, due to the low occurrence of CRISPR systems in the species studied and the low immunity to their phages, thus ensuring greater sensitivity.

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References

Abby, S., B. Néron., H. Ménager., M. Touchon and E. Rocha. 2014. MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems. PloS one. 9(10): e110726.
Abouelhoda, M., S. Kurtz and E. Ohlebusch. 2004. Replacing suffix trees with enhanced suffix arrays. J. Discrete Algorithms. 2(1): 53-86.
Aguirre, G., J. Sánchez, R. Pérez, A. Palacios, T. Trujillo and N. de la Cruz. 2010. Pathogenicity and infection route of Vibrio parahaemolyticus in american white shrimp, Litopenaeus vannamei. J. World Aquac. Soc. 41(3): 464-470.
Alagappan, K., D. Deivasigamani, S. Somasundaram and S. Kumaran. 2010. Occurrence of Vibrio parahaemolyticus and its specific phages from shrimp ponds in east coast of India. Curr. Microbiol. 61(4): 235-240.
Barrangou, R. and P. Horvath. 2017. A decade of discovery: CRISPR functions and applications. ‎Nat. Microbiol. 2(7): 17092.
Benson, D., I. Karsch, D. Lipman., J. Ostell and D. Wheeler. 2008. GenBank. Nucleic Acids Res. 36(Database issue): D25.
Bernal, A., U. Ear and N. Kyrpides. 2001. Genomes OnLine Database (GOLD): a monitor of genome projects world-wide. Nucleic Acids Res. 29(1): 126-127.
Box, A., M. McGuffie., B. O'Hara and K. Seed. 2016. Functional analysis of bacteriophage immunity through a type I-E CRISPR/Cas system in Vibrio cholerae and its application in bacteriophage genome engineering. J. Bacteriol. 198(3): 578-590.
Chakraborty, S., T. Waise., F. Hassan., Y. Kabir., M. Smith and M. Arif. 2009. Assessment of the Evolutionary Origin and Possibility of CRISPR-Cas (CASS) Interference Pathway in Vibrio cholerae O395. In silico biology. 9(4): 245-254.
Cheng, L., J. Huang, C. Shi, K. Thompson, B. Mackey and J. Cai. 2008. Vibrio parahaemolyticus associated with mass mortality of postlarval abalone, Haliotis diversicolor supertexta (L.), in Sanya, China. J. World Aquac. Soc. 39(6): 746-757.
Grissa, I., G. Vergnaud and C. Pourcel. 2007a. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 35 (suppl 2): W52-W57.
Grissa, I., G. Vergnaud and C. Pourcel. 2007b. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics. 8(1):172.
Horvath, P., A. Coûté., D. Romero, P. Boyaval., C. Fremaux and R. Barrangou. 2009. Comparative analysis of CRISPR loci in lactic acid bacteria genomes. ‎Int. J. Food. Microbiol. 131(1): 62-70.
Horvath, P. and R. Barrangou. 2010. CRISPR/Cas, the immune system of bacteria and archaea. Science. 327(5962): 167-170.
Hyatt, D., G. Chen., P. LoCascio., M. Land., F. Larimer and L. Hauser. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC bioinformatics. 11(1): 119.
Kalatzis, P., D. Castillo, P. Katharios and M. Middelboe. 2018. Bacteriophage interactions with marine pathogenic Vibrios: Implications for phage therapy. Antibiot. 7(1): 15.
Kurtz, S and C. Schleiermacher. 1999. REPuter: fast computation of maximal repeats in complete genomes. Bioinformatics (Oxford, England), 15(5): 426-427.
Labbate, M., F. Orata., N. Petty., N. Jayatilleke., W. King., P. Kirchberger and Y. Boucher. 2016. A genomic island in Vibrio cholerae with VPI-1 site-specific recombination characteristics contains CRISPR-Cas and type VI secretion modules. Sci. Rep. 6: 36891.
Larkin, M., G. Blackshields., N. Brown., R. Chenna., P. McGettigan., H. McWilliam and J.Thompson, J. D. 2007. Clustal W and Clustal X version 2.0. Bioinformatics. 23(21): 2947-2948.
Lomelí, C. and S. Martínez. 2014. Phage therapy against Vibrio parahaemolyticus infection in the whiteleg shrimp (Litopenaeus vannamei) larvae. Aquaculture. 434: 208-211.
Lyons, C., N. Raustad., M. Bustos and M. Shiaris. 2015. Incidence of Type II CRISPR1-Cas Systems in Enterococcus Is Species-Dependent. PloS one. 10(11): e0143544.
Makarova, K., Y. Wolf., O. Alkhnbashi., F. Costa., S. Shah., S. Saunders and P. Horvath. 2015. An updated evolutionary classification of CRISPR–Cas systems. Nat. Rev. Microbiol. 13(11): 722.
Oliveira, J., F. Castilho., A. Cunha and M. Pereira. 2012. Bacteriophage therapy as a bacterial control strategy in aquaculture. Aquacult. Int. 20(5): 879-910.
Rice, L. and Stokes, L. 2008. Federal Funding for the study of antimicrobial resistance in nosocomial pathogens: No ESKAPE. National Institute of Allergy and Infectious Diseases. 197(8): 1079-1081.
São, C. 2018. Engineering of phage-derived lytic enzymes: Improving their potential as antimicrobials. Antibiot. 7(2): 29.
Shen, J., L. Lv., X. Wang., Z. Xiu and G. Chen. 2017. Comparative analysis of CRISPR‐Cas systems in Klebsiella genomes. J. Basic Microbiol. 57(4): 325-336.
Sun, H., Y. Li., X. Shi., Y. Lin., Y. Qiu., J. Zhang and Q. Sun. 2015. Association of CRISPR/Cas evolution with Vibrio parahaemolyticus virulence factors and genotypes. Foodborne Pathog Dis. 12(1): 68-73.
Tamura, K., G. Stecher., D. Peterson, A. Filipski and S. Kumar. 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol. 30(12): 2725-2729.
Yooseph, S., K. Nealson., D. Rusch., J. McCrow., C. Dupont., M. Kim., J. Johnson., R. Montgomery., S. Ferriera and K. Beeson. 2010. Genomic and functional adaptation in surface ocean planktonic prokaryotes. Nature. 468(7320): 60-66.
Won, K. and S. Park. 2008. Pathogenicity of Vibrio harveyi to cultured marine fishes in Korea. Aquaculture. 285(1-4): 8-13.
Published
2021-03-15
How to Cite
Parra, Ángel, Lossada, C., Pérez, A., Navarrete, J., & González, L. (2021). Characterization of CRISPR genetic sequences in microorganisms associated with infections in shrimp (Litopenaeus vannamei). Revista De La Facultad De Agronomía De La Universidad Del Zulia, 38(2), 360-381. Retrieved from https://produccioncientificaluz.org/index.php/agronomia/article/view/35504
Section
Animal Production