For whole-genome shotgun selleck chemicals llc metagenomics analysis, reads were analysed using the Kraken taxonomic classifier software with the supplied minikraken database.34 Reads from the metagenomics data set were aligned to P. aeruginosa Clade E as in the previous section and phylogenetic placement was carried out using pplacer in conjunction with FastTree.35 Sequence data is available
from the European Nucleotide Archive for the Illumina data (ERP006056) and the corrected Pacific Biosciences assembly (ERP006058). Results Study results Recruitment lasted a period of 300 days, ending according to protocol after the enrolment of 30 screening patients. In total, we detected P. aeruginosa in five patients. Of these patients, three had P. aeruginosa detected only in burns wound swabs, one had P. aeruginosa detected in their burns wound and in their urine, and one had P. aeruginosa in their sputum. One additional eligible patient did
not consent to enter the study and was excluded. The average age in the study group was 41 years. Males predominated with a male-to-female ration of 2.3:1. Flame burns were the most common mechanism of injury, followed by scalds and mixed flame/flash injuries. The average burn size of the study group was 12.5% of the TBSA and 27% of patients sustained an inhalation injury. Eight patients required admission to intensive trauma unit (ITU) and the majority required surgical treatment of their burns with excision and skin grafting (80%). A large majority of the study group (83%) received shower cart hydrotherapy as a routine part of their wound management to encourage healing through wound debridement and decontamination. The average length of hospital stay (LOS) was 17 days and taking into account burn size, the average was 1.4 days per % TBSA. The water and environment in burns and critical care units are frequently colonised by P. aeruginosa
A total of 282 water and environmental samples were screened for P. aeruginosa of which 39/78 (50%) were positive in water samples, 25/96 (26%) were positive from the wet environment and 7/108 (6%) were positive from the dry environment. A total of 86 genome sequences were generated from the 71 positives, as in some cases multiple colony picks were sequenced. Seventy-eight patient samples were screened for P. aeruginosa of which 39 (50%) were positive. A total of 55 genome sequences were Batimastat generated, as in some cases multiple colony picks were sequenced. In total, 141 genomes were sequenced; water and environmental (n=86) and patient (n=55). Genomes were sequenced to a mean coverage of 24.4×, with the minimum coverage of a sample being 14× and highest 64.7×. When placed in the context of a global collection of P. aeruginosa strains, phylogenetic reconstruction demonstrated isolates in our study fell into eight clades (figure 1A).