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Background   Blastocystis  sp .  are among the most commonly observed intestinal parasites in routine clinical parasitology.  Blastocystis  in humans consists of at least 9 genetic subtypes. Different subtypes of  Blastocystis  may be associated with differences in pathogenicity and symptomatology.    Methods  Advanced microscopy on two samples and sequence-confirmed PCR on a third sample from the same individual were used for  Blastocystis  diagnosis and subtype analyses on routine clinical samples in a university hospital.    Results  With a combined gold standard of sequence-confirmed PCR and positive advanced microscopy, 107 out of 442 (24.2%) patients were diagnosed with  Blastocystis . infection, which is a high frequency of detection in comparison to previous reports from industrialized countries. The sensitivity of microscopy and sequence-confirmed PCR was 99.1% (106/107) and 96.3% (103/107), respectively.  Among 103 typable samples, subtype 3 was most abundant (n = 43, 42%), followed by subtypes 1 and 2 (both n = 23, 22%), subtype 4 (n = 12, 12%), and single samples with subtypes 6 (1%) and subtype 7 (1%). The prevalence of  Blastocystis  infection was 38% in patients from the Department of Tropical Medicine and 18% in patients from other departments.    Conclusions  A high prevalence of  Blastocystis  infection was found with both advanced microscopy and sequence-confirmed PCR in our patient population. Most cases were caused by subtypes ST1, ST2, ST3 and ST4. A significantly higher prevalence was found among patients with a history of recent travel to tropical countries.

Diagnosis and subtype analysis of Blastocystis sp.in 442 patients in a hospital setting in the Netherlands