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

2021

Lane, Courtney R

Brett, Judith

Schultz, Mark

Gorrie, Claire L

Stevens, Kerrie

Cameron, Donna R M

St George, Siobhan

van Diemen, Annaliese

Easton, Marion

Stuart, Rhonda L

Sait, Michelle

Peleg, Anton Y

Stewardson, Andrew J

Cheng, Allen C

Spelman, Denis W

Waters, Mary Jo

Ballard, Susan A

Sherry, Norelle L

Williamson, Deborah A

Romanes, Finn

Sutton, Brett

Kwong, Jason C

Seemann, Torsten

Goncalves da Silva, Anders

Stephens, Nicola

Howden, Benjamin P

Antimicrobial resistance

Carbapenemase producing Enterobacterales

Public Health Surveillance

genomics

infection control

Journal Article

0000-0002-7789-8360

10.1093/cid/ciaa972

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). 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 program's first three years (January 2016 to December 2018). 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. 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.

link

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021; 73(11): e3912-e3920

Clinical Infectious Diseases