Regional Spread of bla _NDM-1-Containing Klebsiella pneumoniae ST147 in Post-Acute Care Facilities

Abstract

Background

Carbapenem-resistant Enterobacterales (CRE) harboring bla _KPC have been endemic in Chicago-area healthcare networks for more than a decade. During 2016–2019, a series of regional point-prevalence surveys identified increasing prevalence of bla _NDM-containing CRE in multiple long-term acute care hospitals (LTACHs) and ventilator-capable skilled nursing facilities (vSNFs). We performed a genomic epidemiology investigation of bla _NDM-producing CRE to understand their regional emergence and spread.

Methods

We performed whole-genome sequencing on New Delhi metallo-beta-lactamase (NDM)+ CRE isolates from 4 point-prevalence surveys across 35 facilities (LTACHs, vSNFs, and acute care hospital medical intensive care units) in the Chicago area and investigated the genomic relatedness and transmission dynamics of these isolates over time.

Results

Genomic analyses revealed that the rise of NDM+ CRE was due to the clonal dissemination of an sequence type (ST) 147 Klebsiella pneumoniae strain harboring bla _NDM-1 on an IncF plasmid. Dated phylogenetic reconstructions indicated that ST147 was introduced into the region around 2013 and likely acquired NDM around 2015. Analyzing the relatedness of strains within and between facilities supported initial increases in prevalence due to intrafacility transmission in certain vSNFs, with evidence of subsequent interfacility spread among LTACHs and vSNFs connected by patient transfer.

Conclusions

We identified a regional outbreak of bla _NDM-1 ST147 that began in and disseminated across Chicago area post-acute care facilities. Our findings highlight the importance of performing genomic surveillance at post-acute care facilities to identify emerging threats.

Abstract

Whole-genome sequencing of carbapenem-resistant Enterobacterales in Chicago area healthcare facilities revealed clonal dissemination of bla _NDM-1 Klebsiella pneumoniae sequence type 147 within and between post-acute care facilities.