Defining a genomic threshold for investigating Pseudomonas aeruginosa hospital outbreak
Sara Romano-Bertrand, Maxine Virieux-Petit, Florian Mauffrey, Laurence Senn, Dominique Blanc
Abstract
BACKGROUND: When investigating Pseudomonas aeruginosa (PA) outbreaks, the clonality of isolates should be demonstrated using a molecular typing method. Whole-genome sequencing (WGS) is the new gold standard for bacterial genotyping, but care should be taken in the interpretation of results regarding considering isolates as part of the same chain of transmission. AIM: To determine genomic threshold to identify recent transmission events considering the spatiotemporal scale of the outbreak. METHODS: PA outbreaks occurring in our hospital during the past 15 years were retrospectively analysed by both core-genome MLST and single-nucleotide polymorphism (SNP) with regard to epidemiological data. Our results were discussed in the light of previous published literature employing WGS to investigate hospital outbreaks of PA. FINDINGS: Fourteen investigations of PA outbreaks in our hospital were included, lasting a few days to nine years. Isolates belonging to the same chain of transmission presented up to 13 loci differences and 25 SNPs. These results were in accordance with the 19 published outbreaks that mostly reported a similarity among epidemiologically related isolates below 15-25 SNPs. The impact of time and space on the threshold of eligible SNPs or loci differences was possibly masked by other factors including the genotype, the number of isolates included in the WGS analysis, the path of transmission and the presence of environmental reservoir. CONCLUSIONS: Our study emphasizes the need to integrate genomic thresholds with epidemiological data, especially when environmental reservoirs or hypermutators are involved, to accurately assess transmission dynamics and outbreak origins.