Table 1.

General advantages and disadvantages of diagnostic platforms broadly available at present for mollusc pathogens.

assay	advantages	disadvantages
gross pathology	allows rapid preliminary assessment in systems where specific gross signs are commonly associated with infection (e.g. mikrocytosis in C. gigas, Brown Ring Disease in R. philippinarum)	few pathogens are associated with relatively unambiguous gross signs of disease
paraffin histopathology	provides excellent perspective on animal health; allows detection of multiple infections and emerging disease events; technology widely available	slow; requires specialized expertise; can be insensitive for detection of small pathogens (e.g. Bonamia); not suitable for viruses and bacteria
cytology, tissue imprints	rapid and inexpensive; useful for specific evaluation of haemolymph and haemocytes for Bonamia, of digestive gland imprints for Marteilia	not considered effective for detection of Perkinsus or Haplosporidium parasites; not useful for bacteria, viruses
Ray's fluid thioglycollate method	rapid and inexpensive; useful for specific evaluation of tissue samples for most Perkinsus parasites; can be quantitative	only specific to Perkinsus species
transmission electron microscopy	allows ultrastructural description; suitable for distinguishing parasites belonging to different genera (e.g. Bonamia from Mikrocytos) and sometimes congeneric species, identifying and characterizing viral infections	expensive, slow; requires specialized expertise and technology that is not universally available; focus on very small tissue areas could result in pathogens being missed
PCR, conventional	relatively rapid; required skills common in students of biology; technology widely available; can be more sensitive for detection of small pathogens that are difficult to visualize microscopically; specificity can be ‘tuned’ to be broad or narrow	provides indirect and imperfect perspective on animal health; positive results only indicate presence of pathogen DNA, not necessarily viable pathogen or actual infection; requires substantial background knowledge of the genetics of targeted (and ideally, related) pathogens
PCR, quantitative	same as conventional PCR, but with added advantages of pathogen quantitation, greater speed and likely sensitivity; with validation quantitation may allow stronger inferences about actual infection than are possible with conventional PCR	Same as conventional PCR; platform more expensive, less widely available than for conventional PCR and requires greater expertise for proper interpretation; copy number of target imperfectly correlated with infection intensity
ISH	best single method for linking a DNA sequence to pathogen observed in tissue sections; as with PCR, sensitivity can be tuned; requires histopathology but more sensitive than conventional histopathology for detection of small cryptic pathogens	(very) slow, very specialized
DNA sequencing	constitutes the definitive identification of pathogen DNA sequences	same as quantitative PCR; requires PCR amplification first, which is not always straightforward for detection or characterization of new pathogens
next-generation sequencing	allows rapid profiling of pathogen diversity	expensive, with technology not universally available; requires substantial bioinformatics expertise and resources; as for PCR, positive results not clearly indicative of actual infection