Use Of Next-Generation Sequencing To Rule Out Cluster Of Pseudomonas Aeruginosa In A Cardiac Critical Care Unit

Background: In spring of 2019, 2 positive sputum cases of Pseudomonas aeruginosa in the cardiac critical care unit (CCU) were reported to the UFHJ infection prevention (IP) department. The initial 2 cases, detected within 3 days of each other, were followed shortly by a third case. Epidemiological evidence was initially consistent with a hospital-acquired infection (HAI): 2 of the 3 patients roomed next to each other, and all 3 patients were ventilated, 2 of whom shared the same respiratory therapist. However, no other changes in routine or equipment were noted. The samples were cultured and processed using Illumina NGS technology, generating 1–2 million short (ie, 250-bp) reads across the P. aeruginosa genome. As an additional positive control, 8 P . aeruginosa NGS data sets, previously shown to be from a single outbreak in a UK facility, were included. Reads were mapped back to a reference sequence, and single-nucleotide polymorphisms (SNPs) between each sample and the reference were extracted. Genetic distances (ie, the number of unshared SNPs) between all UFHJ and UK samples were calculated. Genetic linkage was determined using hierarchical clustering, based on a commonly used threshold of 40 SNPs. All UFHJ patient samples were separated by >18,000 SNPs, indicating genetically distinct samples from separate sources. In contrast, UK samples were separated from each other by <16 SNPs, consistent with genetic linkage and a single outbreak. Furthermore, the UFHJ samples were separated from the UK samples by >17,000 SNPs, indicating a lack of geographical distinction of the UFHJ samples (Fig. 1). These results demonstrated that while the initial epidemiological evidence pointed towards a single HAI, the high-precision and relatively inexpensive (