Studies on infectious and emerging diseases caused by bats have been increasing worldwide due to their well-recognised status as a reservoir species for various infectious agents as well as their close relationship to humans and animals. This study reports the molecular frequency and diversity of the parasites belonging to the Sarcocystidae family in bats in São Paulo state, Brazil. A total of 2892 tissue samples (brain and pectoral muscle/heart homogenates) from 1921 bats belonging to 36 species were collected, and the Sarcocystidae protozoan 18S ribosomal RNA encoding genes (18S rDNA) were detected by nested PCR and Sanger sequencing. The relative prevalence of Sarcocystidae species was 4.7% (91/1921) among 16 bat species, including insectivorous (n = 65), frugivorous (n = 13) and nectarivorous (n = 11) bats. From 66 sequenced positive samples, 50 were found to be suitable for analysis. Ten samples from insectivorous and nectarivorous bats showed 100% similarity with Neospora caninum (n = 1), Hammondia hammondi (n = 1), Cystoisospora canis (n = 1), Nephroisospora eptesici (n = 1), Sarcocystis (Frenkelia) glareoli (n = 1), and Toxoplasma gondii (n = 5). The 45 non-T. gondii samples revealed 15 different 18S rDNA alleles with identities varying from 96.1 to 100% with several Sarcocystidae species, which might suggest that bats can harbour a large variety of Sarcocystidae organisms. From the five T. gondii-positive tissue samples, three samples from two different bat specimens of the insectivorous Eumops glacinus were characterised using 11 PCR-restriction fragment length polymorphism (RFLP) markers, revealing the non-archetypal ToxoDB genotypes #6 (type BrI), which is one of the most prevalent in different hosts and regions from Brazil, and #69. We recommend the inclusion of T. gondii as a differential diagnosis for rabies and other neurological syndromes in bats.

蝙蝠引起的传染病和新出现疾病的研究在世界范围内得到了发展，这是由于蝙蝠作为各种传染原的储库物种的公认地位以及与人类和动物的密切关系。这项研究报告了巴西圣保罗州蝙蝠中属于Sarcocystidae科的寄生虫的分子频率和多样性。总共收集了来自19个蝙蝠的2892个组织样本（大脑和胸肌/心脏匀浆物），它们属于36个物种，并且通过巢式PCR和Sanger测序检测到了囊尾虫的原生动物18S核糖体RNA编码基因（18S rDNA）。Sarcocystidae种类的相对发生率是4.7％（1921分之91）中16个蝙蝠物种，包括食虫（Ñ  = 65），食果（Ñ = 13）和肉食性（n  = 11）蝙蝠。从66个测序的阳性样品中，发现50个适合分析。十个食虫和食肉蝙蝠样品显示与新孢子虫（n  = 1），Hammondia hammondi（n  = 1），Cystoisospora canis（n  = 1），Nephroisospora eptesici（n  = 1），Sarcocystis（Frenkelia）glareoli（100％）相似n  = 1）和弓形虫（n  = 5）。45个非弓形虫样本揭示了15种不同的18S rDNA等位基因，其与几种肉蝇科的同一性从96.1％到100％不等，这可能表明蝙蝠可以藏有多种肉蝇科的生物。从11个PCR限制性片段长度多态性（RFLP）标记中，从5个刚地弓形虫阳性组织样本中，从食虫性Eumops glacinus的两个不同蝙蝠样本中提取了3个样本，揭示了非原型ToxoDB基因型＃6（BrI类型），它是来自巴西的不同寄主和地区中最普遍的流行音乐之一，排名第69。我们建议将刚地弓形虫作为蝙蝠中狂犬病和其他神经系统综合症的鉴别诊断。