Publication
Genomic interrogation of the burden and transmission of multidrug-resistant pathogens within and across hospital networks
Publisher:
Cold Spring Harbor Laboratory
Date:
10-09-2019
DOI:
10.1101/764787
Abstract: Multidrug-resistant organisms (MDROs) disproportionately affect hospitalized patients due to the combination of comorbidities, frequent antimicrobial use, and in-hospital MDRO transmission. Identification of MDRO transmission by hospital microbiology laboratories is difficult due to limitations of existing typing methods. We conducted a prospective multicenter genomics implementation study (8 hospitals, 2800 beds) from 24 th April to 18 th June 2017 in Melbourne, Australia. Clinical and screening isolates from hospital inpatients were collected for six MDROs ( vanA VRE, MRSA, ESBL E. coli [ESBL-Ec] and Klebsiella pneumoniae [ESBL-Kp], and carbapenem-resistant Pseudomonas aeruginosa [CRPa] and Acinetobacter baumannii [CRAb]), sequenced (Illumina NextSeq) and analyzed using open-source tools. MDRO transmission was assessed by genomics (core SNP phylogeny, grouped by species and ST) and compared to epidemiologic data. 408 isolates were collected from 358 patients 47.5% were screening isolates. ESBL-Ec was most common (52.5%), then MRSA (21.6%), vanA VRE (15.7%) and ESBL-Kp (7.6%). We define the transmission rate for each MDRO by genomics and epidemiology 31.6% of all study patients had potential genomic links to other study isolates 86% of these were confirmed by epidemiologic links (probable or possible transmission). The highest transmission rates occurred with van A VRE (88.4% of patients). Combining genomics with high-quality epidemiologic data gives substantial insights into the burden and distribution of critical MDROs in hospitals, including in-hospital transmission. By defining transmission rates by genomics, we hope to enable comparisons over time and between sites, and introduce this as a new outcome measure to assess the efficacy of infection control interventions.