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Background   Taenia solium ,  T. asiatica  and  T. saginata  tapeworms cause human taeniasis and are the origin of porcine and bovine cysticercosis. Furthermore,  T. solium  eggs can cause human cysticercosis, with neurocysticercosis being the most serious form of the disease. These helminth infections are neglected tropical diseases and are endemic in several countries in the Americas, Asia and Africa. As a result of globalization, migration in particular, the infections have been extending to non-endemic territories. Species-specific diagnosis of taeniasis is subject to drawbacks that could be resolved using molecular approaches. In the present study, conventional and real-time amplification protocols (cPCR and qPCR) based on the  T. saginata  HDP2 sequence were applied in the differential diagnosis of taeniasis ( T. saginata ,  T. solium ) in both fecal samples and proglottids expelled by patients. The HDP2 homolog in  T. solium  was cloned and characterized.    Results  Semi-nested cPCR and qPCR (Sn-HDP2 cPCR and Sn-HDP2 qPCR) amplified  T. saginata  and  T. solium  DNA, with an analytical sensitivity of 40 and 400 fg, respectively, and identically in both protocols. Eighteen taeniasis patients were diagnosed directly with  T. saginata  or  T. solium , either from proglottids or fecal samples with/without eggs (detected using microscopy), based on the optimized Sn-HDP2 qPCR. After cloning, the  T. solium  HDP2 homolog sequence was confirmed to be a ribosomal sequence. The HDP2 fragment corresponded to a non-transcribed sequence/external transcribed repeat (NTS/ETS) of ribosomal DNA. Compared with the  T. saginata  HDP2 homolog, the  T solium  HDP2 sequence lacked the first 900 nt at the 5′ end and showed nucleotide substitutions and small deletions.    Conclusions  Sn-HDP2 cPCR and Sn-HDP2 qPCR were set up for the diagnosis of human taeniasis, using proglottids and fecal samples from affected patients. The new Sn-HDP2 qPCR protocol was the best option, as it directly differentiated  T. saginata  from  T. solium . The diagnosis of an imported  T. solium -taeniasis case and nine European  T. saginata  cases was relevant. Finally, the cloning and sequencing of the  T. solium  HDP2 fragment confirmed that HDP2 was part of a ribosomal unit.    Electronic supplementary material  The online version of this article (10.1186/s13071-018-2646-6) contains supplementary material, which is available to authorized users.

HDP2: a ribosomal DNA (NTS-ETS) sequence as a target for species-specific molecular diagnosis of intestinal taeniasis in humans