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Search and contain: Impact of an integrated genomic and epidemiological surveillance and response program for control of carbapenemase-producing Enterobacterales

Citation

Lane, CR and Bret, J and Schultz, M and Gorrie, CL and Stevens, K and Cameron, DRM and St George, S and van Diemen, A and Easton, M and Stuart, RL and Sait, M and Peleg, AY and Stewardson, AJ and Cheng, AC and Spelman, DW and Waters, MJ and Ballard, SA and Sherry, NL and Williamson, DA and Romanes, F and Sutton, B and Kwong, JC and Seemann, T and Goncalves da Silva, A and Stephens, N and Howden, BP, Search and contain: Impact of an integrated genomic and epidemiological surveillance and response program for control of carbapenemase-producing Enterobacterales, Clinical Infectious Diseases ISSN 1058-4838 (2020) [Refereed Article]


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Copyright Statement

© The Author(s) 2020. Published by Oxford University Press for the Infectious Diseases Society of America. Licensed under Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) http://creativecommons.org/licenses/by-nc-nd/4.0/

DOI: doi:10.1093/cid/ciaa972

Abstract

Background: Multi-resistant organisms (MROs) pose a critical threat to public health. Population-based programs for control of MROs such as Carbapenemase-producing Enterobacterales (CPE) have emerged and evaluation is needed. We assess the feasibility and impact of a state-wide CPE surveillance and response program deployed in December 2015 across Victoria, Australia (population 6.5 million).

Methods: A prospective multi-modal intervention including active screening, carrier isolation, centralised case investigation and comparative pathogen genomics was implemented. We analyze trend in CPE incidence and clinical presentation, risk factors and local transmission over the programís first three years (January 2016 to December 2018).

Results: CPE case ascertainment increased over the study period to 1.42 cases/100,000 population, linked to increased screening without a concomitant rise in active clinical infections (0.45-0.60 infections/100,000 population, p=0.640). KPC-2 infection decreased from 0.29 infections/100,000 population prior to intervention to 0.03 infections/100,000 population in 2018 (p=0.003). Comprehensive case investigation identified putative overseas community acquisition. Median time between isolate referral and initial genomic and epidemiological assessment for local transmission was 11 days (IQR 9-14). Prospective surveillance identified numerous small transmission networks (median 2, range 1-19 cases), predominantly IMP and KPC, with median pairwise distance of 8 (IQR 4-13) single nucleotide polymorphisms; low diversity between clusters of the same sequence type suggested genomic cluster definitions alone are insufficient for targeted response.

Conclusions: We demonstrate the value of centralised CPE control programs to increase case ascertainment, resolve risk factors and identify putative local transmission through prospective genomic and epidemiological surveillance; methodologies are transferable to low-prevalence settings and MROs globally.

Item Details

Item Type:Refereed Article
Keywords:antimicrobial resistance, public health surveillance, carbapenemase producing <i>Enterobacterales</i>, infection control, genomics
Research Division:Health Sciences
Research Group:Epidemiology
Research Field:Epidemiology not elsewhere classified
Objective Division:Health
Objective Group:Public health (excl. specific population health)
Objective Field:Disease distribution and transmission (incl. surveillance and response)
UTAS Author:Stephens, N (Dr Nicola Stephens)
ID Code:140023
Year Published:2020
Deposited By:Medicine
Deposited On:2020-07-22
Last Modified:2021-08-12
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