Gastrointestinal helminths of terrestrial small mammals in West Africa

Study Extent

Sampling sites of seven countries of sub-Saharan Africa (Benin, Burkina Faso, Guinea, Mali, Mauritania, Niger, and Senegal), corresponding to various environments (districts of cities, villages, field borders, orchards, savannas, or forests).

Sampling

Gastrointestinal helminths were collected from the digestive tracts of small mammals that had been unrolled and stored in plasitic universal vials containing 95% ethanol. Each digestive tract was carefully scrutinised for helminths along its different sections (stomach, small intestine, large intestine and caecum) following Ribas et al. 2011. Gastrointestinal helminths were carefully removed, then classified by taxon (at the genus, family, order, class or phylum level) according to the knowledge of the person in charge of this work and to morphological characteristics observable at the binocular.

Quality Control

Several samples were idenfied more thoroughly at the genus or species level combining morphological and molecular approaches as diagnostic tools. Morphological identification was carried out using conventional microscopy and generalist identification keys (Khalil et al., 1994; Anderson et al., 2009) or specific literature when available, with the involvement of specialist collaborators when possible (Alexis Ribas, Jerzy Behnke and Malick Diouf, Voitto Haukisalmi). For most identified taxa, at least one specimen* was identified per small mammal species was sequenced for cytochrome oxidase 1 (cox1) for nematodes and acanthocephalans, and nicotinamide adenine dinucleotide subunit 1 (NAD1) for cestodes (Diagne et al. 2016). This precise identification was done for seven Acanthocephala, 157 Cestoda, and 541 Nematoda.
Additional data about the host individual (sex, body size, reproductive characteristics) are registered in the CBGP small mammal database (BPM, http://bpm-cbgp.science). All samples of the dataset are included in the CBGP reference collection of small mammals (https://doi.org/10.15454/WWNUPO).

Method steps

1. Ethical guidelines and standards have been followed at every single step of the data collection and transfer. Prior explicit agreement from relevant local authorities and individual owners was systematically obtained for each sampling campaign within private dwellings. Trapping sessions and transfer of biological samples were carried out in accordance with requirements of local and French legislations. We systematically received an explicit approval from the relevant institutional comitee (Centre de Biologie pour la Gestion des Populations (CBGP): Agrement pour l’utilisation d’animaux à des fins scientifiques D-34-169-1) for all protocols used to handle biological materials. We also ensured that any animal-related procedure was performed according to official ethical guidelines provided by the American Society of Mammalogists (Sikes and Gannon 2011). None of the rodent species investigated here has any protected status from the International Union for Conservation of Nature. The dataset is an extraction of the BPM database - internal Small Mammal database of the laboratory CBGP (Centre de Biologie pour la Gestion des Populations) to manage data and preserve specimen involved : field campain data, taxonomic data, sequenced data

5270 samples (each of them being composed of 1 to several individuals of a given taxon) of gastrointestinal helminths were collected from 4116 small mammals* from at least 38 species belonging to 17 genera of rodents (mostly Muridae, but also some Dipodidae, Gliridae, Nesomyidae, and Sciuridae; many of them being identified at the species level (following Happold 2013) using morphological, molecular and/or chromosomal data), and to two species of shrews (Soricidae). Gastrointestinal helminths that were collected covered three taxonomic phyla (Nematoda, Platyhelminthes and Acanthocephala). Among the 2950 samples classified as Nematoda, 1606 were identified at the genus level and 236 were identified at the species level. Among the 2163 samples classified as Cestoda, 115 were identifed at the genus level and 149 at the species level. The 34 samples of Trematoda remain unidentified. Among the 32 samples classified as Acanthocephala, seven were identified at the species level. Five hundred thirty-three samples remain either unclassified due to the insufficient quality of materials to be unambiguously scrutinized, or to be identified as the recorded samples are progressively identified using morphological and/or molecular tools.

1. Acanthocephala
   rank: phylum
2. Anatrichosoma
   rank: genus
3. Anatrichosoma gerbillis
   rank: species
4. Aspiculuris
   rank: genus
5. Aspiculuris africana
   rank: species
6. Aspiculuris tetraptera
   rank: species
7. Capillaria
   rank: genus
8. Cestoda
   rank: class
9. Enoplida
   rank: order
10. Gongylonema
    rank: genus
11. Heligmonina
    rank: genus
12. Hymenolepis
    rank: genus
13. Hymenolepis diminuta
    rank: species
14. Hymenolepis stramina
    rank: species
15. Mastophorus
    rank: genus
16. Mathevotaenia
    rank: genus
17. Mathevotaenia symmetrica
18. Moniliformis moniliformis
    rank: species
19. Nematoda
    rank: phylum
20. Neoheligmonella granjoni
    rank: species
21. Oxynema
    rank: genus
22. Oxynema xerusi
    rank: species
23. Oxyuridae
    rank: family
24. Oxyuroidea
    rank: superfamily
25. Physaloptera
    rank: genus
26. Protospirura
    rank: genus
27. Protospirura muricola
    rank: species
28. Pseudophysaloptera
    rank: genus
29. Pterygodermatites
    rank: genus
30. Pterygodermatites niameyiensis
    rank: species
31. Pterygodermatites senegalensis
    rank: species
32. Raillietina
    rank: genus
33. Raillietina (Raillietina) baeri
    rank: species
34. Raillietina (Raillietina) trapezoides
    rank: species
35. Skrjabinotaenia
    rank: genus
36. Spiruridae
    rank: family
37. Subulura
    rank: genus
38. Syphacia
    rank: genus
39. Syphacia obvelata
    rank: species
40. Syphatineria
    rank: genus
41. Trematoda
    rank: class
42. Trichostrongylidae
    rank: family
43. Trichostrongyloidea
    rank: superfamily
44. Trichuris
    rank: genus
45. Trichuris duplantieri
    rank: species
46. Trichuris mastomysi
    rank: species
47. Platyhelminthes
    rank: phylum

The data were collected in seven countries of Sahelo-Sudanian Africa: Benin (3 sampling sites), Burkina Faso (5 sampling sites), Guinea (2 sampling sites), Mali (37 sampling sites), Mauritania (10 sampling sites), Niger (25 sampling sites, of which 19 were different districts from Niamey), and Senegal (205 sampling sites)