Search and Contain: Impact of an Integrated Genomic and Epidemiological Surveillance and Response Program for Control of Carbapenemase-producing Enterobacterales

Courtney R. Lane, Judith Brett, Mark Schultz, Claire L. Gorrie, Kerrie Stevens, Donna R. M. Cameron, Siobhan St George, Annaliese van Diemen, Marion Easton, Rhonda L. Stuart, Michelle Sait, Anton Y. Peleg, Andrew J. Stewardson, Allen C. Cheng, Denis Spelman, Mary Jo Waters, Susan A. Ballard, Norelle L. Sherry, Deborah A. Williamson, Finn RomanesBrett Sutton, Jason C. Kwong, Torsten Seemann, Anders Goncalves da Silva, Nicola Stephens, Benjamin P. Howden

Research output: Contribution to journalArticleResearchpeer-review

9 Citations (Scopus)


Background: Multiresistant 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 assessed the feasibility and impact of a statewide CPE surveillance and response program deployed across Victoria, Australia (population 6.5 million). Methods: A prospective multimodal intervention including active screening, carrier isolation, centralized case investigation, and comparative pathogen genomics was implemented. We analyzed trends in CPE incidence and clinical presentation, risk factors, and local transmission over the program's first 3 years (2016-2018). Results: CPE case ascertainment increased over the study period to 1.42 cases/100000 population, linked to increased screening without a concomitant rise in active clinical infections (0.45-0.60 infections/100000 population, P=.640). KPC-2 infection decreased from 0.29 infections/100000 population prior to intervention to 0.03 infections/100000 population in 2018 (P=.003). Comprehensive case investigation identified instances of overseas community acquisition. Median time between isolate referral and 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 centralized CPE control programs to increase case ascertainment, resolve risk factors, and identify local transmission through prospective genomic and epidemiological surveillance; methodologies are transferable to low-prevalence settings and MROs globally.

Original languageEnglish
Pages (from-to)e3912-e3920
Number of pages9
JournalClinical Infectious Diseases
Issue number11
Publication statusPublished - Dec 2021


  • antimicrobial resistance
  • carbapenemase-producing Enterobacterales
  • genomics
  • infection control
  • public health surveillance

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