Improving the specific diagnosis of trematode, cestode and nematode infections by a multiplex single-tube real-time PCR assay

J Clin Pathol. 2019 Jul;72(7):487-492. doi: 10.1136/jclinpath-2018-205590. Epub 2019 Apr 5.


Aims: Helminth infections are becoming uncommon in high-income countries and laboratory staff may lose expertise in their morphological identification, especially in histological sections where speciation of helminths is challenging. Commercially available molecular diagnostic panels for faecal specimens only offer tests for protozoa but not helminths. We aim to improve the identification accuracy of helminths using a multiplex PCR assay.

Methods: We designed three pairs of PCR primers and probes targeting multicopy genes for a multiplex single-tube real-time PCR assay which covers 16 trematode (28S rRNA gene), 24 cestode (cox1 gene) and 33 nematode (cox1 gene) species. Helminths (n=27) from faecal samples (n=10), fresh parasites (n=11), formalin-fixed specimens (n=4), cerebrospinal fluid (n=1) and bile (n=1) were examined morphologically and tested by PCR. Fifty stool samples negative for parasites by microscopy were also tested.

Results: The PCR assay correctly identified the genera of all tested helminths. Agarose gel electrophoresis and sequencing of the purified PCR amplicons confirmed that the PCR products were of correct sizes with 100% correlation with the respective species. Sequencing of the cox1 gene failed to identify Capillaria spp. in one sample owing to the lack of corresponding sequences in GenBank. PCR and sequencing of the nematode 18S rRNA gene using consensus primers showed 100% homology with Capillaria spp. sequence. No positive PCR products were found in the negative stool samples.

Conclusions: The highly specific test correctly identified all helminths in our cohort. It is a useful adjunct to helminth identification in difficult situations such as histological sections.

Keywords: diagnostics; infections; microbiology; parasites.

MeSH terms

  • Animals
  • Base Sequence
  • Cestoda / genetics
  • Cestoda / isolation & purification*
  • Cestode Infections / diagnosis*
  • Cestode Infections / parasitology
  • Cohort Studies
  • DNA Primers / genetics
  • DNA, Protozoan / chemistry
  • DNA, Protozoan / genetics
  • DNA, Ribosomal / chemistry
  • DNA, Ribosomal / genetics
  • Feces / parasitology
  • Humans
  • Multiplex Polymerase Chain Reaction / methods*
  • Nematoda / genetics
  • Nematoda / isolation & purification*
  • Nematode Infections / diagnosis*
  • Nematode Infections / parasitology
  • Real-Time Polymerase Chain Reaction / methods
  • Sensitivity and Specificity
  • Sequence Alignment
  • Trematoda / genetics
  • Trematoda / isolation & purification*
  • Trematode Infections / diagnosis*
  • Trematode Infections / parasitology


  • DNA Primers
  • DNA, Protozoan
  • DNA, Ribosomal