Table 1.
Details of the Leptospira-positive samples from terrestrial small mammals and bats used in the analyses, the number of genetic sequences obtained, and the associated Leptospira spp
| Order: family | Species | No. of samples | Nb of sequences | Leptospira sp | ||
| rrs2 | secY | MLST5 | ||||
| Madagascar | ||||||
| Rodentia: Nesomyidae | Eliurus minor | 15 | 15 | 13 | 13 | Lb |
| Afrotheria: Tenrecidae | Hemicentetes nigriceps | 1 | 1 | 1 | 1 | Lk |
| Hemicentetes semispinosus | 1 | 1 | 1 | 0 | Lk | |
| Microgale cowani | 2 | 2 | 2 | 1 | Lb, Lm | |
| Microgale dobsoni | 5 | 5 | 4 | 4 | Lm | |
| Microgale longicaudata | 1 | 1 | 1 | 1 | Lb | |
| Microgale majori | 2 | 2 | 2 | 2 | Lb | |
| Microgale principula | 2 | 2 | 2 | 2 | Lb | |
| Chiroptera: Vespertilionidae | Myotis goudoti | 1 | 1 | 1 | 1 | Lb |
| Chiroptera: Miniopteridae | Miniopterus gleni | 1 | 1 | 1 | 1 | Lb |
| Miniopterus griffithsi | 1 | 1 | 1 | 1 | Lb | |
| Miniopterus mahafaliensis | 3 | 3 | 3 | 3 | Lb | |
| Miniopterus majori | 1 | 1 | 1 | 0 | Lb | |
| Miniopterus sororculus | 1 | 1 | 1 | 0 | Lb | |
| Chiroptera: Molossidae | Otomops madagascariensis | 1 | 1 | 1 | 1 | Lb* |
| Mormopterus jugularis | 2 | 2 | 2 | 1 | Lb* | |
| Chiroptera: Pteropodidae | Pteropus rufus | 1 | 1 | 0 | 0 | Lsp |
| Chiroptera: Rhinonycteridae | Triaenops menamena | 5 | 5 | 5 | 3 | Li, Lb*, Lsp |
| Tanzania | ||||||
| Rodentia: Nesomyidae | Cricetomys sp. | 7 | 7 | 7 | 7 | Lb, Lk |
| Rodentia: Muridae | Mastomys sp. | 5 | 5 | 5 | 5 | Li, Lb |
| Soricomorpha: Soricidae | Crocidura sp. | 11 | 11 | 11 | 11 | Li, Lb |
| Mayotte | ||||||
| Rodentia: Muridae | *Rattus rattus | 8 | 8 | 8 | 8 | Li, Lb |
| Afrotheria: Tenrecidae | *Tenrec ecaudatus | 8 | 8 | 8 | 8 | Lm |
| Seychelles | ||||||
| Rodentia: Muridae | *Rattus rattus | 1 | 1 | 1 | 1 | Li |
| Chiroptera: Pteropodidae | Pteropus seychellensis | 1 | 1 | 0 | 0 | Lsp |
| La Réunion | ||||||
| Rodentia: Muridae | *Rattus rattus | 3 | 3 | 2 | 2 | Li |
| Chiroptera: Molossidae | Mormopterus francoismoutoui | 4 | 4 | 4 | 4 | Lb* |
| Union of the Comoros | ||||||
| Chiroptera: Miniopteridae | Miniopterus griveaudi | 1 | 1 | 1 | 1 | Lb |
| Chiroptera: Pteropodidae | Rousettus obliviosus | 2 | 2 | 1 | 1 | Li, Lb |
| Mauritius | ||||||
| Chiroptera: Molossidae | Mormopterus acetabulosus | 8 | 8 | 8 | 7 | Lb* |
| South Africa | ||||||
| Chiroptera: Vespertilionidae | Glauconycteris variegata | 1 | 1 | 0 | 0 | Lk |
| Scotophilus dinganii | 1 | 1 | 1 | 1 | Lb | |
| Chiroptera: Miniopteridae | Miniopterus natalensis | 8 | 8 | 7 | 6 | Lb, Lk |
| Chiroptera: Nycteridae | Nycteris thebaica | 2 | 2 | 2 | 2 | Lb |
| Chiroptera: Pteropodidae | Rousettus aegyptiacus | 8 | 8 | 5 | 1 | Li, Lb* |
| Swaziland | ||||||
| Chiroptera: Nycteridae | Nycteris thebaica | 1 | 0 | 1 | 0 | Li |
| Mozambique | ||||||
| Chiroptera: Miniopteridae | Miniopterus mossambicus | 1 | 1 | 1 | 1 | Lb |
| Total | 127 | 126 | 115 | 101 | ||
MLST5 includes the rrs2, secY, adk, lipL41, and icdA genes. The identification of the different Leptospira species is based on single (Figure S2 and S3) and concatenated gene phylogenies (Fig. 3). Introduced species are designated with an asterisk. Two endemic lineages of terrestrial small mammals occur on Madagascar, which include the family Tenrecidae and the subfamily Nesomyinae of the family Nesomyidae. The genus Cricetomys belongs to a separate subfamily, the Cricetomyinae, of the Nesomyidae
Li=L. interrogans, Lb = L. borgpetersenii, Lb* = sequences closely related to L. borgpetersenii, Lm = L. mayottensis, Lk = L. kirschneri. Lsp corresponds to unidentified Leptospira species.