Detecting Carbapenemases in Animal and Food Samples by Droplet Digital PCR

Background: The presence of carbapenemase-producing bacteria (CPB) in animal hosts and along the food chain may result in the development of reservoirs for human infections. Several CPB strains isolated from animals have been reported, suggesting that transmission and dissemination of the corresponding genes between humans and animals may occur. Animal and food samples have complex backgrounds that hinder the detection of CPB present in low concentrations by standard detection procedures. Methods: We evaluated the possibility of detecting bla(KPC), bla(VIM), and bla(OXA-48)-like carbapenemases in 286 animal and food samples (faeces from farm and companion animals, raw meat, bivalve molluscs) by culture-based and standard molecular methods and by ddPCR. Results: The proposed ddPCR managed to detect the target genes, also in samples resulting negative to standard methods. While the presence of bla(KPC) and bla(VIM) was detected in few samples (similar to 3%), one third of the samples (n = 94/283) carried different variants of bla(OXA-48)-like genes. Conclusion: A specific and sensitive method such as ddPCR could be suitable to evaluate the current veterinarian and environmental situation and to assess the dynamic transmission and persistence of CPB between animals and humans and vice versa.

Automated summary

The study successfully detected carbapenemase genes in animal and food samples using ddPCR, even in samples that tested negative using standard methods. Many samples carried different variants of the bla(OXA-48)-like genes. ddPCR could be a suitable method for evaluating the transmission and persistence of carbapenemase-producing bacteria between animals and humans.