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Trypanosome diversity in wildlife species from the serengeti and Luangwa Valley ecosystems.

Auty H, Anderson NE, Picozzi K, Lembo T, Mubanga J, Hoare R, Fyumagwa RD, Mable B, Hamill L, Cleaveland S, Welburn SC - PLoS Negl Trop Dis (2012)

Bottom Line: In addition to Trypanosoma brucei, T. congolense, T. simiae, T. simiae (Tsavo), T. godfreyi and T. theileri, three variants of T. vivax were identified from three different wildlife species within one ecosystem, including sequences from trypanosomes from a giraffe and a waterbuck that differed from all published sequences and from each other, and did not amplify with conventional primers for T. vivax.Wildlife carries a wide range of trypanosome species.The failure of the diverse T. vivax in this study to amplify with conventional primers suggests that T. vivax may have been under-diagnosed in Tanzania.

View Article: PubMed Central - PubMed

Affiliation: Centre for Infectious Diseases, College of Medicine and Veterinary Medicine, The University of Edinburgh, Edinburgh, United Kingdom.

ABSTRACT

Background: The importance of wildlife as reservoirs of African trypanosomes pathogenic to man and livestock is well recognised. While new species of trypanosomes and their variants have been identified in tsetse populations, our knowledge of trypanosome species that are circulating in wildlife populations and their genetic diversity is limited.

Methodology/principal findings: molecular phylogenetic methods were used to examine the genetic diversity and species composition of trypanosomes circulating in wildlife from two ecosystems that exhibit high host species diversity: the Serengeti in Tanzania and the Luangwa Valley in Zambia. Phylogenetic relationships were assessed by alignment of partial 18S, 5.8S and 28S trypanosomal nuclear ribosomal DNA array sequences within the Trypanosomatidae and using ITS1, 5.8S and ITS2 for more detailed analysis of the T. vivax clade. In addition to Trypanosoma brucei, T. congolense, T. simiae, T. simiae (Tsavo), T. godfreyi and T. theileri, three variants of T. vivax were identified from three different wildlife species within one ecosystem, including sequences from trypanosomes from a giraffe and a waterbuck that differed from all published sequences and from each other, and did not amplify with conventional primers for T. vivax.

Conclusions/significance: Wildlife carries a wide range of trypanosome species. The failure of the diverse T. vivax in this study to amplify with conventional primers suggests that T. vivax may have been under-diagnosed in Tanzania. Since conventional species-specific primers may not amplify all trypanosomes of interest, the use of ITS PCR primers followed by sequencing is a valuable approach to investigate diversity of trypanosome infections in wildlife; amplification of sequences outside the T. brucei clade raises concerns regarding ITS primer specificity for wildlife samples if sequence confirmation is not also undertaken.

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Related in: MedlinePlus

Neighbour-joining tree based on partial 18S, 5.8S and partial 28S trypanosomatid sequences.Bodo caudatus was included as an outgroup. Bootstrap values are shown where support is >70%. Sequences generated in this study are shown in blue (identified sequences in dark blue, unidentified sequences in light blue), and labelled with sample identity; pathogen species (UnK if unknown); host species; Genbank ID. Other sequences were retrieved from Genbank and are shown in black, and are labelled with pathogen species and Genbank ID. T. brucei clade indicated in grey box.
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pntd-0001828-g001: Neighbour-joining tree based on partial 18S, 5.8S and partial 28S trypanosomatid sequences.Bodo caudatus was included as an outgroup. Bootstrap values are shown where support is >70%. Sequences generated in this study are shown in blue (identified sequences in dark blue, unidentified sequences in light blue), and labelled with sample identity; pathogen species (UnK if unknown); host species; Genbank ID. Other sequences were retrieved from Genbank and are shown in black, and are labelled with pathogen species and Genbank ID. T. brucei clade indicated in grey box.

Mentions: Phylogenetic analyses were conducted to infer the relationships of sequences generated in this study with other trypanosomes. The partial 18S, 5.8S and partial 28S sequences were aligned using the ClustalW [31] accessory application in Bioedit, followed by visual optimisation (it was not possible to align the ITS1 and ITS2 regions across all variants found, due to their hypervariability). In addition to all sequences generated in this study, included in the alignment were sequences listed in Genbank for this region within the T. brucei clade; we use T. brucei clade to refer to the clade which includes T. brucei, T. congolense, T. simiae, T. godfreyi and T. vivax and related subspecies and groups, as by [32]: only one sequence each was available for T. congolense savannah, forest and Kilifi, T. simiae, T. simiae Tsavo and T. godfreyi; for T. brucei one representative sequence was included; for T. vivax, one clone of each of the seven available published sequences was used. In addition, published sequences from outside the T. brucei clade but within the Trypanosomatidae were included to help identify more diverse sequences. Accession numbers for all reference sequences are included in Figure 1. A neighbour-joining tree was constructed using Geneious [33] under a Hasegawa-Kishino-Yano (HKY) [34] model of substitution. Bodo caudatus was included as an outgroup; B. caudatus is a member of the Bodonidae, another kinetoplastid family, and has been shown to be a valid outgroup for trypanosomatids [32]. Confidence in branching relationships was assessed using bootstrap re-sampling over 1000 replicates. Using the same alignment, trees were also constructed in PAUP * 4.0 [35] using minimum evolution and maximum likelihood optimality criteria, both with an HKY model of substitution and default settings for the heuristic searches conducted.


Trypanosome diversity in wildlife species from the serengeti and Luangwa Valley ecosystems.

Auty H, Anderson NE, Picozzi K, Lembo T, Mubanga J, Hoare R, Fyumagwa RD, Mable B, Hamill L, Cleaveland S, Welburn SC - PLoS Negl Trop Dis (2012)

Neighbour-joining tree based on partial 18S, 5.8S and partial 28S trypanosomatid sequences.Bodo caudatus was included as an outgroup. Bootstrap values are shown where support is >70%. Sequences generated in this study are shown in blue (identified sequences in dark blue, unidentified sequences in light blue), and labelled with sample identity; pathogen species (UnK if unknown); host species; Genbank ID. Other sequences were retrieved from Genbank and are shown in black, and are labelled with pathogen species and Genbank ID. T. brucei clade indicated in grey box.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3475651&req=5

pntd-0001828-g001: Neighbour-joining tree based on partial 18S, 5.8S and partial 28S trypanosomatid sequences.Bodo caudatus was included as an outgroup. Bootstrap values are shown where support is >70%. Sequences generated in this study are shown in blue (identified sequences in dark blue, unidentified sequences in light blue), and labelled with sample identity; pathogen species (UnK if unknown); host species; Genbank ID. Other sequences were retrieved from Genbank and are shown in black, and are labelled with pathogen species and Genbank ID. T. brucei clade indicated in grey box.
Mentions: Phylogenetic analyses were conducted to infer the relationships of sequences generated in this study with other trypanosomes. The partial 18S, 5.8S and partial 28S sequences were aligned using the ClustalW [31] accessory application in Bioedit, followed by visual optimisation (it was not possible to align the ITS1 and ITS2 regions across all variants found, due to their hypervariability). In addition to all sequences generated in this study, included in the alignment were sequences listed in Genbank for this region within the T. brucei clade; we use T. brucei clade to refer to the clade which includes T. brucei, T. congolense, T. simiae, T. godfreyi and T. vivax and related subspecies and groups, as by [32]: only one sequence each was available for T. congolense savannah, forest and Kilifi, T. simiae, T. simiae Tsavo and T. godfreyi; for T. brucei one representative sequence was included; for T. vivax, one clone of each of the seven available published sequences was used. In addition, published sequences from outside the T. brucei clade but within the Trypanosomatidae were included to help identify more diverse sequences. Accession numbers for all reference sequences are included in Figure 1. A neighbour-joining tree was constructed using Geneious [33] under a Hasegawa-Kishino-Yano (HKY) [34] model of substitution. Bodo caudatus was included as an outgroup; B. caudatus is a member of the Bodonidae, another kinetoplastid family, and has been shown to be a valid outgroup for trypanosomatids [32]. Confidence in branching relationships was assessed using bootstrap re-sampling over 1000 replicates. Using the same alignment, trees were also constructed in PAUP * 4.0 [35] using minimum evolution and maximum likelihood optimality criteria, both with an HKY model of substitution and default settings for the heuristic searches conducted.

Bottom Line: In addition to Trypanosoma brucei, T. congolense, T. simiae, T. simiae (Tsavo), T. godfreyi and T. theileri, three variants of T. vivax were identified from three different wildlife species within one ecosystem, including sequences from trypanosomes from a giraffe and a waterbuck that differed from all published sequences and from each other, and did not amplify with conventional primers for T. vivax.Wildlife carries a wide range of trypanosome species.The failure of the diverse T. vivax in this study to amplify with conventional primers suggests that T. vivax may have been under-diagnosed in Tanzania.

View Article: PubMed Central - PubMed

Affiliation: Centre for Infectious Diseases, College of Medicine and Veterinary Medicine, The University of Edinburgh, Edinburgh, United Kingdom.

ABSTRACT

Background: The importance of wildlife as reservoirs of African trypanosomes pathogenic to man and livestock is well recognised. While new species of trypanosomes and their variants have been identified in tsetse populations, our knowledge of trypanosome species that are circulating in wildlife populations and their genetic diversity is limited.

Methodology/principal findings: molecular phylogenetic methods were used to examine the genetic diversity and species composition of trypanosomes circulating in wildlife from two ecosystems that exhibit high host species diversity: the Serengeti in Tanzania and the Luangwa Valley in Zambia. Phylogenetic relationships were assessed by alignment of partial 18S, 5.8S and 28S trypanosomal nuclear ribosomal DNA array sequences within the Trypanosomatidae and using ITS1, 5.8S and ITS2 for more detailed analysis of the T. vivax clade. In addition to Trypanosoma brucei, T. congolense, T. simiae, T. simiae (Tsavo), T. godfreyi and T. theileri, three variants of T. vivax were identified from three different wildlife species within one ecosystem, including sequences from trypanosomes from a giraffe and a waterbuck that differed from all published sequences and from each other, and did not amplify with conventional primers for T. vivax.

Conclusions/significance: Wildlife carries a wide range of trypanosome species. The failure of the diverse T. vivax in this study to amplify with conventional primers suggests that T. vivax may have been under-diagnosed in Tanzania. Since conventional species-specific primers may not amplify all trypanosomes of interest, the use of ITS PCR primers followed by sequencing is a valuable approach to investigate diversity of trypanosome infections in wildlife; amplification of sequences outside the T. brucei clade raises concerns regarding ITS primer specificity for wildlife samples if sequence confirmation is not also undertaken.

Show MeSH
Related in: MedlinePlus