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Open AccessArticle

PCR-RFLP Detection and Genogroup Identification of Piscirickettsia salmonis in Field Samples

1
Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago 7830490, Chile
2
FONDAP Center for Genome Regulation, Santiago 8370415, Chile
3
Laboratorio Especialidades Técnicas Marinas (ETECMA), Puerto Montt 5500001, Chile
*
Author to whom correspondence should be addressed.
Current address: Laboratorio de Genética y Genómica de Interacciones Biológicas (LG2IB), Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile.
Pathogens 2020, 9(5), 358; https://doi.org/10.3390/pathogens9050358
Received: 4 April 2020 / Revised: 28 April 2020 / Accepted: 30 April 2020 / Published: 8 May 2020
(This article belongs to the Section Animal Pathogens)
Piscirickettsia salmons, the causative agent of piscirickettsiosis, is genetically divided into two genomic groups, named after the reference strains as LF-89-like or EM-90-like. Phenotypic differences have been detected between the P. salmonis genogroups, including antibiotic susceptibilities, host specificities and pathogenicity. In this study, we aimed to develop a rapid, sensitive and cost-effective assay for the differentiation of the P. salmonis genogroups. Using an in silico analysis of the P. salmonis 16S rDNA digestion patterns, we have designed a genogroup-specific assay based on PCR-restriction fragment length polymorphism (RFLP). An experimental validation was carried out by comparing the restriction patterns of 13 P. salmonis strains and 57 field samples obtained from the tissues of dead or moribund fish. When the bacterial composition of a set of field samples, for which we detected mixtures of bacterial DNA, was analyzed by a high-throughput sequencing of the 16S rRNA gene amplicons, a diversity of taxa could be identified, including pathogenic and commensal bacteria. Despite the presence of mixtures of bacterial DNA, the characteristic digestion pattern of the P. salmonis genogroups could be detected in the field samples without the need of a microbiological culture and bacterial isolation. View Full-Text
Keywords: Piscirickettsia salmonis; polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP); LF-89-like; EM-90-like; 16S rDNA sequencing Piscirickettsia salmonis; polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP); LF-89-like; EM-90-like; 16S rDNA sequencing
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Aravena, P.; Pulgar, R.; Ortiz-Severín, J.; Maza, F.; Gaete, A.; Martínez, S.; Serón, E.; González, M.; Cambiazo, V. PCR-RFLP Detection and Genogroup Identification of Piscirickettsia salmonis in Field Samples. Pathogens 2020, 9, 358.

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