Two laboratories did not achieve a good performance in the initial 2018 quality control test on Salmonella typing, according to a new report.
The National Reference Laboratories (NRLs) of EU member states participate in quality control tests which consist of proficiency tests on Salmonella. Performance is assessed annually by testing ability to identify 20 Salmonella strains. The objective is to evaluate if typing of Salmonella strains by labs was done uniformly, and whether comparable results were being obtained.
As well as the standard method for typing Salmonella which is serotyping, 12 labs performed typing at DNA level using Pulsed Field Gel Electrophoresis (PFGE).
While the labs were not identified, one was an EU NRL and the other a non-EU NRL. One of them reported a serotyping frequency of daily with 6,000 strains serotyped in 2018 and 450 strains PFGE typed. The other lab recorded a frequency of three times a week with 400 strains serotyped in 2018.
The follow-up study for serotyping in March and April 2019 involved typing an additional set of 10 Salmonella strains. Results showed both participants achieved a good performance. The criterion for this performance is less than four penalty points, which are given for incorrect typing of strains. No EU NRLs got a “non-good” performance in the 2016 or 2017 studies.
Serotyping and PFGE results
EU-candidate nations Albania, Republic of North Macedonia and Serbia, EFTA countries Iceland, Norway and Switzerland, and Israel took part in the 2018 assessment which is organized by the European Union Reference Laboratory (EURL) for Salmonella. The EURL-Salmonella is at the National Institute for Public Health and the Environment (RIVM) in the Netherlands.
All 36 labs performed serotyping. The O-antigens were typed correctly by 28 of the 35 participants. This corresponds to 98 percent of the total number of strains. The H-antigens were typed correctly by 23 of 35 labs, corresponding to 97 percent of the number of strains. As a result, 20 participants gave the correct serovar names, corresponding to 96 percent of all strains evaluated.
Serotyping of Salmonella Cannstatt (1,3,19:m,t:-) caused the most problems in the study with 10 participants having issues.
For the sixth and final time, the study also included PFGE typing. PFGE is a more detailed typing method sometimes needed to trace the source of a contamination. For quality control, participants received another 11 strains of Salmonella to be tested by this method. Ten of 12 labs were equipped to use the PFGE method.
Overall, 82 percent of the scores were good or excellent. However, two of the 12 images resulted in a poor score on at least one of seven parameters. The two images would be unsuitable for inter-laboratory database comparison of these PFGE profiles, according to the report.
ECDC Salmonella assessment
Findings from a different Salmonella typing assessment have also been published by the European Centre for Disease Prevention and Control (ECDC).
It was for public health national reference labs in ECDC’s Food- and Waterborne Diseases and Zoonoses network (FWD-Net) and arranged by the Statens Serum Institut in Denmark between June and October 2018.
Salmonellosis was the second-most common zoonotic disease in EU in 2017 with more than 90,000 cases. From 2008 to 2017, a decreasing trend of confirmed cases was observed for 25 countries that consistently reported during the period. However, during 2013 to 2017, the overall trend did not show any significant increase or decrease.
This round assessed the ability of labs to perform multiple-locus variable number of tandem repeat analysis (MLVA) for Salmonella Enteritidis and to identify a cluster based on molecular typing by PFGE, MLVA and/or whole genome sequencing (WGS) derived data.
Out of the 26 participants who signed up, 23 completed it and submitted their results.
Ten of 23 labs performed the MLVA typing of Salmonella Typhimurium, however only two reported correct allelic profiles for all 10 test isolates. Ten out of the 23 participants did MLVA typing of Salmonella Enteritidis and seven recorded the correct allelic profiles for all test isolates.
The number of participants in MLVA for Salmonella Typhimurium was lower than previous years. This reflects a trend, where more labs are switching to WGS-based surveillance and outbreak detection using WGS instead of MLVA, according to ECDC.
Thirteen participants performed the cluster analysis using PFGE-derived data and nine correctly identified the cluster of closely related isolates.
Several incorrect results and challenges of the PFGE method, highlight the problem that many labs still use, and probably will continue to use, the PFGE method for several years. The added value of this method is to bridge the historical PFGE databases with WGS data, according to the report.
Twelve labs performed cluster analysis using WGS-derived data and 10 correctly identified the cluster of closely related isolates among the 12 test isolates.
There are difficulties in inter-laboratory comparability between member states regarding surveillance and outbreak investigation when different methods are used, according to the report. Despite increasing use of WGS as a typing tool for large outbreaks, many labs still use PFGE for primary surveillance and outbreak investigation.
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