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

Abstract

Background Carbapenem-resistant Enterobacterales (CRE) harboring blaKPC 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 blaNDM-containing CRE in multiple long-term acute care hospitals (LTACHs) and ventilator-capable skilled nursing facilities (vSNFs). We performed a genomic epidemiology investigation of blaNDM-producing CRE to understand their regional emergence and spread. Methods We performed whole-genome sequencing on NDM+ CRE isolates from four 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 ST147 Klebsiella pneumoniae strain harboring blaNDM-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 intra-facility transmission in certain vSNFs, with evidence of subsequent inter-facility spread among LTACHs and vSNFs connected by patient transfer. Conclusions We identified a regional outbreak of blaNDM-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.

Whole-Genome Sequencing (WGS) of Carbapenem-Resistant K. pneumoniae Isolated in Long-Term Care Facilities in the Northern Italian Region

“…One reason for the rapid dissemination of K. pneumoniae is the presence of antibiotic resistance genes in mobile genetic elements and the Inc-groups, which belong to plasmids IncF, IncFII(K1), IncR, IncX, IncX3, IncI2, and ColE1 [15][16][17][18][19]. However, carbapenem-resistant K. pneumoniae strains are not only confined to healthcare settings, but also to the community and among residents of LTCFs [20][21][22][23][24]. In Italy, the carbapenem-resistant Enterobacterales from LTCFs have been reported since 2010 in different endemic areas [25][26][27][28].…”

regentrans: a framework and R package for using genomics to study regional pathogen transmission

“…Please refer to the references noted in for a detailed description of the methods and algorithms used in the underlying functions [3, 4, 6–8].…”

“…A powerful tool for studying regional pathogen transmission is whole-genome sequencing, which allows us to investigate pathogen movements at very high resolution [4, 6]. Several studies have used whole-genome sequencing, sometimes paired with additional epidemiological metadata, to gain insights into locations [6, 7] and drivers [3, 4, 8] of elevated intra- or inter-facility transmission. These types of analyses have the potential to transform our public health response to MDROs if they are regularly performed at, or in collaboration with, regional public health centres.…”

regentrans: a framework and R package for using genomics to study regional pathogen transmission

“…The required and optional inputs to each function, as well as a reference to a manuscript that uses the method, can be found in Table 1. Each of the references describes in more detail the algorithm used in the underlying function [3,4,6,7,21]. Many functions require a phylogenetic tree read in by ape::read.tree() and/or a pairwise SNV distance matrix calculated using ape::dist.dna(), which requires a DNAbin object input that can be read in using ape::read.fasta().…”

“…A powerful tool for studying regional pathogen transmission is whole-genome sequencing, which allows us to investigate pathogen movements at very high resolution [4, 6]. Several studies have used whole-genome sequencing, sometimes paired with additional epidemiological metadata, to gain insights into locations [6, 7] and drivers [3, 4, 8] of elevated intra- or inter-facility transmission. These types of analyses have the potential to transform our public health response to MDROs if they are regularly performed at, or in collaboration with, regional public health centers.…”