Carbapenemase-producing Salmonella from non-human sources in Germany: An update

Between 2012 and 2017, Germany challenged the occurrence of a VIM-1 carbapenemase producing (CP) S. Infantis clone in different livestock sectors. Despite aggravated traceability due to few epidemiological data, a swine farm was identified, possibly having contributed to the spread of CP Enterobacteriaceae in Germany. This farm indeed revealed the presence of further VIM-1 encoding Enterobacteriaceae (S. Goldcoast and Enterobacter cloacae).

The German National Reference Laboratory (NRL) for Salmonella, receiving ~4000 Salmonella isolates annually from various non-human sources, set CP Salmonella as another monitoring focus. We implemented several methods for the detection of carbapenemase encoding genes in Salmonella.

Since 2014, all isolates received based on directive 2003/99/EG are tested for their MIC against 3rd generation cephalosporins and meropenem, according to CID 2013/652/EU. Illumina short read WGS assemblies of all Salmonella isolates sequenced in the NRL so far, were subjected to resistome analysis based on AMRFinder database. Isolates neither tested for meropenem via MIC nor subjected to WGS analysis, but belonging to former VIM-1 CP serovars (S. Goldcoast, S. Infantis) or originating from wildlife (due to a unique detection of a NDM-1 producing S. Corvallis from a wild bird in 2012), are tested via real-time PCR covering carbapenemases genes bla_GES, bla_OXA-48, bla_VIM, bla_NDM and bla_KPC.

More than 16.000 Salmonella isolates from food, livestock or wildlife animals were analyzed with at least one of the described methods (MIC, WGS or real-time PCR). In none of the isolates tested, a carbapenemase-encoding gene could be detected via MIC or real-time PCR. WGS data of the more than 5000 Salmonella genomes revealed no further carbapenemase-encoding gene.

Despite diligent analyses, no CP Salmonella isolates were detected in this study. Measures taken at the swine farm tested positive for VIM-1 producing Enterobacteriaceae the years after its identification seem to have been successful. A further spread of the bla_VIM-1 harbouring plasmid in Germany, especially in Salmonella, might have stopped. However, different CP E. coli have been detected in the last years, underlining that this issue should still not be underestimated and needs further attention.