Nanopore MinION Sequencing Reveals Possible Transfer of bla KPC-2 Plasmid Across Bacterial Species in Two Healthcare Facilities.

Catharine Prussing,Pascal Lapierre,Navjot Singh,Kara Mitchell,Emily A Snavely,Wolfgang Haas,Erica Lasek-Nesselquist,Rita Owsiak,Elizabeth Nazarian,Kimberlee A Musser

doi:10.3389/fmicb.2020.02007

Abstract

Carbapenemase-producing Enterobacteriaceae are a major threat to global public health. Klebsiella pneumoniae carbapenemase (KPC) is the most commonly identified carbapenemase in the United States and is frequently found on mobile genetic elements including plasmids, which can be horizontally transmitted between bacteria of the same or different species. Here we describe the results of an epidemiological investigation of KPC-producing bacteria at two healthcare facilities. Using a combination of short-read and long-read whole-genome sequencing, we identified an identical 44 kilobase plasmid carrying the blaKPC–2 gene in four bacterial isolates belonging to three different species (Citrobacter freundii, Klebsiella pneumoniae, and Escherichia coli). The isolates in this investigation were collected from patients who were epidemiologically linked in a region in which KPC was uncommon, suggesting that the antibiotic resistance plasmid was transmitted between these bacterial species. This investigation highlights the importance of long-read sequencing in investigating the relatedness of bacterial plasmids, and in elucidating potential plasmid-mediated outbreaks caused by antibiotic resistant bacteria.

Highlights

Carbapenem-resistant Enterobacteriaceae (CRE) are an urgent global health threat, and have been categorized by the World Health Organization (World Health Organization [WHO], 2017) and the United States Centers for Disease Control and Prevention (CDC) (Centers for Disease Control and Prevention [CDC], 2019a) as top priorities for research, drug discovery, surveillance, and control
Following the identification of two patients with Klebsiella pneumoniae carbapenemase (KPC)-producing bacteria associated with Facility A (Patient 1, Isolate 1: C. freundii; Patient 2, Isolate 2: K. pneumoniae), a retrospective investigation including colonization screening of patients who had been roommates with or who had overlapped on the same unit for three or more days with either of the two source patients was performed
Routine point prevalence surveys were done at Facility A on the affected unit to identify any additional KPC-producing bacteria. 3 months after the initial investigation, Isolate 4 (C. freundii) was recovered from a rectal swab collected from Patient 4, who had recently been admitted to Facility A (Figure 1)

Summary

Introduction

Carbapenem-resistant Enterobacteriaceae (CRE) are an urgent global health threat, and have been categorized by the World Health Organization (World Health Organization [WHO], 2017) and the United States Centers for Disease Control and Prevention (CDC) (Centers for Disease Control and Prevention [CDC], 2019a) as top priorities for research, drug discovery, surveillance, and control. CRE that produce carbapenemases are concerning epidemiologically because carbapenemase genes can be transferred among bacteria via mobile genetic elements, including plasmids (Bonomo et al, 2017). In the United States, the most commonly identified carbapenemase is Klebsiella pneumoniae carbapenemase (KPC), which has become endemic in parts of the country since it was first described in 1996 (Woodworth et al, 2018; Castanheira et al, 2019). Though first identified in K. pneumoniae, the gene encoding KPC has been detected across multiple genera of gram-negative bacteria (Woodworth et al, 2018; Brandt et al, 2019). Tn4401 and blaKPC are often encoded on plasmids (Brandt et al, 2019), but can be found integrated into the bacterial chromosome (Mathers et al, 2017)

Methods

Results

Conclusion