Candida_auris_seq-sc-4554
Candida_auris_seq
Candida auris is a globally emerging multidrug resistant fungal pathogen causing nosocomial transmission. The fungus first caused an outbreak of 56 cases in the UK in the Royal Brompton Hospital, April-July 2016 resulting in the temporary closure of a ward (Schelenz et al 2016). Subsequently PHE have recorded 81 cases from 20 affected ICUs in 5 hospitals across the UK. In collaboration with PHE, we now have isolates from all of these sites of infection and there is an urgent need to sequence a UK-wide panel of isolates in order to (i) establish who-infects-who and (ii) to determine broader global patterns of nosocomical transmission. WORK TO DATE: We have sequenced 24 isolates of C. auris from the Brompton outbreak using Hiseq and Nanopore, and under active collaboration with the US CDC we have integrated these data to show that the Brompton outbreak is closely related to those isolates from India/Pakistan. A microreact of the project to date can be seen athttps://microreact.org/project/ryNwuTi6. We now seek to sequence a further 48 UK isolates in order to determine whether there are multiple introductions of this fungus ongoing into the UK, and to link to broader global patterns of transmission. Our genome assembly of C. auris (12 contigs) shows that C. auris is haploid with a genome size of 12.5 Mb and ~119,000 shared SNPs of which 86% are parsimoniously informative. Schelenz et al. Antimicrobial Resistance and Infection Control (2016) 5:35 DOI 10.1186/s13756-016-0132-5       This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
Candida auris is a globally emerging multidrug resistant fungal pathogen causing nosocomial transmission. The fungus first caused an outbreak of 56 cases in the UK in the Royal Brompton Hospital, April-July 2016 resulting in the temporary closure of a ward (Schelenz et al 2016). Subsequently PHE have recorded 81 cases from 20 affected ICUs in 5 hospitals across the UK. In collaboration with PHE, we now have isolates from all of these sites of infection and there is an urgent need to sequence a UK-wide panel of isolates in order to (i) establish who-infects-who and (ii) to determine broader global patterns of nosocomical transmission. WORK TO DATE: We have sequenced 24 isolates of C. auris from the Brompton outbreak using Hiseq and Nanopore, and under active collaboration with the US CDC we have integrated these data to show that the Brompton outbreak is closely related to those isolates from India/Pakistan. A microreact of the project to date can be seen athttps://microreact.org/project/ryNwuTi6. We now seek to sequence a further 48 UK isolates in order to determine whether there are multiple introductions of this fungus ongoing into the UK, and to link to broader global patterns of transmission. Our genome assembly of C. auris (12 contigs) shows that C. auris is haploid with a genome size of 12.5 Mb and ~119,000 shared SNPs of which 86% are parsimoniously informative. Schelenz et al. Antimicrobial Resistance and Infection Control (2016) 5:35 DOI 10.1186/s13756-016-0132-5