An international inter-laboratory study to compare digital PCR with ISO standardized qPCR assays for the detection of norovirus GI and GII in oyster tissue

An optimized digital RT-PCR (RT-dPCR) assay for the detection of human norovirus GI and GII RNA was compared with ISO 15216-conform quantitative real-time RT-PCR (RT-qPCR) assays in an interlaboratory study (ILS) among eight laboratories. A duplex GI/GII RT-dPCR assay, based on the ISO 15216-oligonucleotides, was used on a Bio-Rad QX200 platform by six laboratories. Adapted assays for Qiagen Qiacuity or ThermoFisher QuantStudio 3D were used by one laboratory each. The ILS comprised quantification of norovirus RNA in the absence of matrix and in oyster tissue samples. On average, results of the RT-dPCR assays were very similar to those obtained by RT-qPCR assays. The coefficient of variation (CV%) of norovirus GI results was, however, much lower for RT-dPCR than for RT-qPCR in intra-laboratory replicates (eight runs) and between the eight laboratories. The CV% of norovirus GII results was in the same range for both detection formats. Had in-house prepared dsDNA standards been used, the CV% of norovirus GII could have been in favor of the RT-dPCR assay. The ratio between RT-dPCR and RT-qPCR results varied per laboratory, despite using the distributed RT-qPCR dsDNA standards. The study indicates that the RT-dPCR assay is likely to increase uniformity of quantitative results between laboratories.

Aphanomyces astaci in wild crayfish populations in Slovenia: first report of persistent infection in a stone crayfish Austropotamobius torrentium population

All 5 crayfish species inhabiting Slovenian freshwaters, of which 3 are indigenous crayfish species (ICS: Astacus astacus, Austropotamobius pallipes, and A. torrentium) and 2 are non-indigenous (NICS: Pacifastacus leniusculus and Cherax quadricarinatus), were inspected for the presence of Aphanomyces astaci, the causative agent of crayfish plague. Wild crayfish populations showing no clinical signs of infection were inspected using A. astaci-specific real-time PCR. In addition, a conventional PCR assay was employed and confirmative sequencing was performed. Out of 88 analyzed crayfish, 15/27 (55.6%) specimens of A. torrentium from Borovnišcˇ%%KERN_ERR%%ica Brook and 4/35 (11.4%) of P. leniusculus from the Mura River tested positive, showing low to moderate levels of infection (agent levels A1-A4 and A1-A3, respectively). Results revealed the presence of A. astaci not only in the resistant NICS but also in ICS, since the infected population of A. torrentium presumably had no contact with the NICS carrier and appeared to sustain A. astaci infection in the 2 sampling years. Although the A. astaci genotype has not yet been identified, a connection between the latent infection in ICS and a Group A strain of A. astaci, co-evolving with A. torrentium since its first introduction to Slovenia, is suggested as the most plausible conclusion. This is the first reported population of the genus Austropotamobius with persistent infection, in addition to the already known populations of the genus Astacus. Findings of the presumed co-evolution of A. astaci and ICS hosts open new perspectives, necessitating additional studies on the presence of A. astaci genotypes in the persistently infected ICS populations.

Report on overcoming the poor quality of Apai pulsotypes with a short review on PFGE for listeria monocytogenes

Since listeriosis, caused by Listeria monocytogenes, is one of the important concerns of public health in Europe related to foodborne zoonoses, an efficient protocol for isolate typing is necessary when performing epidemiological studies. Three standardized PFGE protocols available for L. monocytogenes were briefly reviewed. Since observing a poor-quality of ApaI pulsotypes in our laboratory, enzymes from three different manufacturers were compared. The obtained pulsotypes showed that restriction digestion with ApaI from New England BioLabs should be complemented with a subsequent overnight incubation of PFGE plugs in TE buffer for better performance.