Mitochondrial and ribosomal markers in the identification of nematodes of clinical and veterinary importance

Abstract Background Nematodes of the Ascarididae, Ancylostomatidae and Onchocercidae families are parasites of human and veterinary importance causing infections with high prevalence worldwide. Molecular tools have significantly improved the diagnosis of these helminthiases, but the selection of genetic markers for PCR or metabarcoding purposes is often challenging because of the resolution these may show. Methods Nuclear 18S rRNA, internal transcribed spacers 1 (ITS-1) and 2 (ITS-2), mitochondrial gene cytochrome oxidase 1 (cox1) and mitochondrial rRNA genes 12S and 16S loci were studied for 30 species of the mentioned families. Accordingly, their phylogenetic interspecies resolution, pairwise nucleotide p-distances and sequence availability in GenBank were analyzed. Results The 18S rRNA showed the least interspecies resolution since separate species of the Ascaris, Mansonella, Toxocara or Ancylostoma genus were intermixed in phylogenetic trees as opposed to the ITS-1, ITS-2, cox1, 12S and 16S loci. Moreover, pairwise nucleotide p-distances were significantly different in the 18S compared to the other loci, with an average of 99.1 ± 0.1%, 99.8 ± 0.1% and 98.8 ± 0.9% for the Ascarididae, Ancylostomatidae and Onchocercidae families, respectively. However, ITS-1 and ITS-2 average pairwise nucleotide p-distances in the three families ranged from 72.7% to 87.3%, and the cox1, 12S and 16S ranged from 86.4% to 90.4%. Additionally, 2491 cox1 sequences were retrieved from the 30 analyzed species in GenBank, whereas 212, 1082, 994, 428 and 143 sequences could be obtained from the 18S, ITS-1, ITS-2, 12S and 16S markers, respectively. Conclusions The use of the cox1 gene is recommended because of the high interspecies resolution and the large number of sequences available in databases. Importantly, confirmation of the identity of an unknown specimen should always be complemented with the careful morphological examination of worms and the analysis of other markers used for specific parasitic groups. Graphical Abstrac

Additional file 1 of Mitochondrial and ribosomal markers in the identification of nematodes of clinical and veterinary importance

Additional file 1: Table S1. Accession numbers of sequences used in the study

Elucidating Spirocerca lupi spread in the Americas by using phylogenetic and phylogeographic analyses

Spirocerca lupi is a parasitic nematode of domestic and wild canids of the world. This nematode induces esophageal spirocercosis and may eventually lead to carcinomas, aortic aneurisms, and death of the animal. Two genotypes of S. lupi have been described based on specimens from Europe, Asia, Africa, and Oceania, but no profound analysis has been conducted with S. lupi from the Americas. To study this, S. lupi specimens isolated from domestic dogs from Mexico, Costa Rica, and the United States, were molecularly characterized using 18S rDNA and cox1 fragments. Bayesian inference (BI) phylogenetic trees, Templeton-Crandall-Sing (TCS) haplotype networks and Principal coordinate analysis on nucleotide distances were constructed for each locus separately. In addition, a phylogeographic study using a fragment of the cox1 gene was used to infer the evolutionary history of the genus. BI cox1 trees grouped S. lupi from the Americas in genotype 1, together with Israeli specimens, and showed a high nucleotide identity with those worms. In the TCS network, American specimens clustered next to Israeli S. lupi. Furthermore, the 18S rDNA gene fragment separated Costa Rican worms from African, Asian, and European specimens and other species of the family Spiruridae. Interestingly, phylogeographic analysis suggested that the origin of S. vulpis was in Europe, and it later diverged into S. lupi that spread first to Africa, then to Asia and finally to the Americas. Therefore, we suggest that the worms from the American continent might have originated from Asia by dispersion of infected intermediate, paratenic or definitive hosts.Universidad de Costa Rica/[803-C2-064]/UCR/Costa RicaUCR::Vicerrectoría de Docencia::Salud::Facultad de MicrobiologíaUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias de la Salud::Centro de Investigación en Enfermedades Tropicales (CIET

Image_1_Elucidating Spirocerca lupi spread in the Americas by using phylogenetic and phylogeographic analyses.jpeg

Spirocerca lupi is a parasitic nematode of domestic and wild canids of the world. This nematode induces esophageal spirocercosis and may eventually lead to carcinomas, aortic aneurisms, and death of the animal. Two genotypes of S. lupi have been described based on specimens from Europe, Asia, Africa, and Oceania, but no profound analysis has been conducted with S. lupi from the Americas. To study this, S. lupi specimens isolated from domestic dogs from Mexico, Costa Rica, and the United States, were molecularly characterized using 18S rDNA and cox1 fragments. Bayesian inference (BI) phylogenetic trees, Templeton-Crandall-Sing (TCS) haplotype networks and Principal coordinate analysis on nucleotide distances were constructed for each locus separately. In addition, a phylogeographic study using a fragment of the cox1 gene was used to infer the evolutionary history of the genus. BI cox1 trees grouped S. lupi from the Americas in genotype 1, together with Israeli specimens, and showed a high nucleotide identity with those worms. In the TCS network, American specimens clustered next to Israeli S. lupi. Furthermore, the 18S rDNA gene fragment separated Costa Rican worms from African, Asian, and European specimens and other species of the family Spiruridae. Interestingly, the phylogeographic analysis suggested that the origin of S. vulpis was in Europe, and it later diverged into S. lupi that spread first to Africa, then to Asia and finally to the Americas. Therefore, we suggest that the worms from the American continent might have originated from Asia by dispersion of infected intermediate, paratenic or definitive hosts.</p

Table_3_Elucidating Spirocerca lupi spread in the Americas by using phylogenetic and phylogeographic analyses.xlsx

Spirocerca lupi is a parasitic nematode of domestic and wild canids of the world. This nematode induces esophageal spirocercosis and may eventually lead to carcinomas, aortic aneurisms, and death of the animal. Two genotypes of S. lupi have been described based on specimens from Europe, Asia, Africa, and Oceania, but no profound analysis has been conducted with S. lupi from the Americas. To study this, S. lupi specimens isolated from domestic dogs from Mexico, Costa Rica, and the United States, were molecularly characterized using 18S rDNA and cox1 fragments. Bayesian inference (BI) phylogenetic trees, Templeton-Crandall-Sing (TCS) haplotype networks and Principal coordinate analysis on nucleotide distances were constructed for each locus separately. In addition, a phylogeographic study using a fragment of the cox1 gene was used to infer the evolutionary history of the genus. BI cox1 trees grouped S. lupi from the Americas in genotype 1, together with Israeli specimens, and showed a high nucleotide identity with those worms. In the TCS network, American specimens clustered next to Israeli S. lupi. Furthermore, the 18S rDNA gene fragment separated Costa Rican worms from African, Asian, and European specimens and other species of the family Spiruridae. Interestingly, the phylogeographic analysis suggested that the origin of S. vulpis was in Europe, and it later diverged into S. lupi that spread first to Africa, then to Asia and finally to the Americas. Therefore, we suggest that the worms from the American continent might have originated from Asia by dispersion of infected intermediate, paratenic or definitive hosts.</p

Table_2_Elucidating Spirocerca lupi spread in the Americas by using phylogenetic and phylogeographic analyses.docx

Spirocerca lupi is a parasitic nematode of domestic and wild canids of the world. This nematode induces esophageal spirocercosis and may eventually lead to carcinomas, aortic aneurisms, and death of the animal. Two genotypes of S. lupi have been described based on specimens from Europe, Asia, Africa, and Oceania, but no profound analysis has been conducted with S. lupi from the Americas. To study this, S. lupi specimens isolated from domestic dogs from Mexico, Costa Rica, and the United States, were molecularly characterized using 18S rDNA and cox1 fragments. Bayesian inference (BI) phylogenetic trees, Templeton-Crandall-Sing (TCS) haplotype networks and Principal coordinate analysis on nucleotide distances were constructed for each locus separately. In addition, a phylogeographic study using a fragment of the cox1 gene was used to infer the evolutionary history of the genus. BI cox1 trees grouped S. lupi from the Americas in genotype 1, together with Israeli specimens, and showed a high nucleotide identity with those worms. In the TCS network, American specimens clustered next to Israeli S. lupi. Furthermore, the 18S rDNA gene fragment separated Costa Rican worms from African, Asian, and European specimens and other species of the family Spiruridae. Interestingly, the phylogeographic analysis suggested that the origin of S. vulpis was in Europe, and it later diverged into S. lupi that spread first to Africa, then to Asia and finally to the Americas. Therefore, we suggest that the worms from the American continent might have originated from Asia by dispersion of infected intermediate, paratenic or definitive hosts.</p

Video_1_Elucidating Spirocerca lupi spread in the Americas by using phylogenetic and phylogeographic analyses.mov

Spirocerca lupi is a parasitic nematode of domestic and wild canids of the world. This nematode induces esophageal spirocercosis and may eventually lead to carcinomas, aortic aneurisms, and death of the animal. Two genotypes of S. lupi have been described based on specimens from Europe, Asia, Africa, and Oceania, but no profound analysis has been conducted with S. lupi from the Americas. To study this, S. lupi specimens isolated from domestic dogs from Mexico, Costa Rica, and the United States, were molecularly characterized using 18S rDNA and cox1 fragments. Bayesian inference (BI) phylogenetic trees, Templeton-Crandall-Sing (TCS) haplotype networks and Principal coordinate analysis on nucleotide distances were constructed for each locus separately. In addition, a phylogeographic study using a fragment of the cox1 gene was used to infer the evolutionary history of the genus. BI cox1 trees grouped S. lupi from the Americas in genotype 1, together with Israeli specimens, and showed a high nucleotide identity with those worms. In the TCS network, American specimens clustered next to Israeli S. lupi. Furthermore, the 18S rDNA gene fragment separated Costa Rican worms from African, Asian, and European specimens and other species of the family Spiruridae. Interestingly, the phylogeographic analysis suggested that the origin of S. vulpis was in Europe, and it later diverged into S. lupi that spread first to Africa, then to Asia and finally to the Americas. Therefore, we suggest that the worms from the American continent might have originated from Asia by dispersion of infected intermediate, paratenic or definitive hosts.</p

Table_1_Elucidating Spirocerca lupi spread in the Americas by using phylogenetic and phylogeographic analyses.docx

Spirocerca lupi is a parasitic nematode of domestic and wild canids of the world. This nematode induces esophageal spirocercosis and may eventually lead to carcinomas, aortic aneurisms, and death of the animal. Two genotypes of S. lupi have been described based on specimens from Europe, Asia, Africa, and Oceania, but no profound analysis has been conducted with S. lupi from the Americas. To study this, S. lupi specimens isolated from domestic dogs from Mexico, Costa Rica, and the United States, were molecularly characterized using 18S rDNA and cox1 fragments. Bayesian inference (BI) phylogenetic trees, Templeton-Crandall-Sing (TCS) haplotype networks and Principal coordinate analysis on nucleotide distances were constructed for each locus separately. In addition, a phylogeographic study using a fragment of the cox1 gene was used to infer the evolutionary history of the genus. BI cox1 trees grouped S. lupi from the Americas in genotype 1, together with Israeli specimens, and showed a high nucleotide identity with those worms. In the TCS network, American specimens clustered next to Israeli S. lupi. Furthermore, the 18S rDNA gene fragment separated Costa Rican worms from African, Asian, and European specimens and other species of the family Spiruridae. Interestingly, the phylogeographic analysis suggested that the origin of S. vulpis was in Europe, and it later diverged into S. lupi that spread first to Africa, then to Asia and finally to the Americas. Therefore, we suggest that the worms from the American continent might have originated from Asia by dispersion of infected intermediate, paratenic or definitive hosts.</p