Surveillance of certain bacterial pathogens was maintained in Germany despite a reduction in sample submissions during the first part of the Coronavirus pandemic, according to the Robert Koch-Institut.

In March 2020, infection control measures were taken in Germany to deal with COVID-19. By August, the number of reported salmonellosis cases was 45.4 percent below the average for the same period from 2015 to 2019. Campylobacter decreased by 22 percent, enterohemorrhagic E. coli (EHEC) infections by 46 percent, shigellosis by 83 percent, listeriosis by 22 percent, and yersiniosis by 7 percent.

The National Reference Center for Salmonella and other bacterial pathogens (NRZ Salm) and the consultant laboratory for Listeria (KL Listeria) at the Robert Koch-Institut (RKI) saw a dro in the number of samples submitted.

The 20 main senders to NRZ Salm and KL Listeria reported being busy with Covid testing but having the capacity to test for bacterial pathogens. However, they received fewer requests for such testing. One reason for this was the decline in visits to the doctor. Another factor was reduced travel abroad.

This finding means a change in the priority of lab analyses due to test requirements for Civid could largely be ruled out as a reason for the decline in bacterial sample submissions, according to scientists.

Despite the number of cases or samples submitted being lower, surveillance of seleced pathogens continued and clusters were identified, they added.

Salmonella and E. coli
In 2020, 264 of 510 analyzed Salmonella Enteritidis isolates could be assigned to 17 clusters. Six clusters had more than 20 isolates. The largest had 44 isolates.

For two multi-country Salmonella Enteritidis outbreaks, very closely related German isolates were identified and submitted to the European Center for Disease Prevention and Control (ECDC).

However, whole genome sequencing (WGS) data needs to be backed up by epidemiological information to identify outbreaks, as clustered isolates by WGS do not automatically mean there is an outbreak.

In 2020, 774 EHEC cultures were analyzed. In spring, several STEC O153 cases were recorded in north-western Germany. NRZ Salm received 19 isolates from an outbreak of E. coli O26:H11 which affected several children’s facilities in Northwest Mecklenburg at the end of November and the beginning of December.

From the end of July to the beginning of October 2020, 50 hemolytic uremic syndrome (HUS) cases were registered, especially in Bavaria and Baden-Württemberg in southern Germany. However, an outbreak was ruled out as from 22 isolates available for sequencing 12 different E. coli types were found and there were no matches from patient samples.

Molecular surveillance revealed 27 small clusters with two to five isolates. In none of them was their evidence of specific foods as a source of infection.

Listeria and Campylobacter
In 2020, KL Listeria received 441 submissions of clinical Listeria monocytogenes isolates from Germany. In total, 259 of the isolates could be assigned to 82 clusters. One cluster had 55 isolates, another had 16, and two had 12.

By comparing sequences with the NRL for Listeria monocytogenes at the German Federal Institute for Risk Assessment (BfR), it was possible to identify food isolates for 26 of the clusters active in 2020.

Four larger Campylobacter clusters were identified, which had 18, 22, 27, and 71 isolates per cluster. Similar isolates from other countries, in particular Denmark and Luxembourg, can be found, so it appears illnesses have occurred across borders, said scientists.