P080

1:Department of Clinical Microbiology and Infectious Diseases, Gregorio Marañón General University Hospital, Madrid, Spain; 2:Gregorio Marañón Health Research Institute (IiSGM), Madrid, Spain; 3:CIBER of Respiratory Diseases (CIBERES), Spain; 4:Doctoral school, Autonomous University of Madrid, Madrid, Spain; 5:Department of Preventive Medicine, Public Health and Epidemiological Surveillance, Poniente University Hospital, Almería, Spain; 6:Doctoral school, University of Alcalá, Spain; 7:Microbiology service, Torrecárdenas Hospital Complex, Almería, Spain; 8:Department of Medicine, Complutense University of Madrid, Madrid, Spain; 9:National Center for Microbiology, Madrid, Spain; 10:Hospital Basurto, Bilbao, Spain

The evolutionary analysis of SNPs within clusters allowed us to distinguish between clusters growing mainly due to reactivations of past exposures and others corresponding to active recent transmission, in which intervention to control is still possible. To optimize the surveillance of active clusters we i) refined the genomic analysis by including repetitive genomic regions and heterozygous calls and ii) accelerated the characterization of new cases by performing nanopore sequencing on primary cultures and/or exploiting suboptimal sequences when sequencing directly on sputa. The usefulness of long-reads in detecting additional diversity was evaluated on a selection of 78 cases from eight long-term clusters. Long-read analysis increased the within cluster diversity (1-22 additional SNPs), thereby enabling the identification of index cases, reconstruct transmission chronologies, and determine the relationships between the cases with greater precision. Secondly, considering not only fixed SNPs but also heterozygous calls (frequency 0.15-0,70) in clusters that demanded higher analytical precision resulted in the proposal of reordering the transmission chronology. Finally, we evaluated whether focusing on key cluster marker-SNPs, we could exploit suboptimal sequences obtained from sputa to rule in/out new cases to pre-existing clusters, when the strain marker-SNPs were sufficiently covered. This rescue strategy enabled not only the assignment of new cases to clusters, but also their location in specific branches of the corresponding genomic networks. The efficacy of this approach was further enhanced by adapting it to a rapid assessment of cases to clusters by calling only specific marker SNPs of the relevant clusters during the nanopore sequencing run.