Confirmation of nosocomial infections using whole-genome sequencing

Between January 2007 and December 2021, we identified six autochthonous malaria cases likely originating from suspicious nosocomial transmissions related to imported malaria patients in France, four of which occurring during the ongoing COVID-19 pandemic. First, we described the clinical history of these events. Then we took advantage of high-throughput sequencing (Illumina) to score parasite genotypes using genome-wide short tandem repeats (STRs) when genomes were sufficiently covered, and genome-wide single-nucleotide polymorphisms (SNPs) for all infections.