Plasmid Dissemination and Selection of a Multidrug-Resistant Klebsiella pneumoniae Strain during Transplant-Associated Antibiotic Therapy

Abstract

Antibiotics, which are used both to prevent and to treat infections, are a mainstay therapy for lifesaving procedures such as transplantation. For this reason, and many others, increased antibiotic resistance among human-associated pathogens, such as the carbapenem-resistant Enterobacteriaceae species, is of grave concern. In this study, we report on a hematopoietic stem cell transplant recipient in whom cultures detected the emergence of carbapenem resistance and spread across five strains of bacteria that persisted for over a year. Carbapenem resistance in Citrobacter freundii, Enterobacter cloacae, Klebsiella aerogenes, and Klebsiella pneumoniae was linked to a pair of plasmids, each carrying the Klebsiella pneumoniae carbapenemase gene (bla_KPC). Surveillance cultures identified a carbapenem-susceptible strain of Citrobacter freundii that may have become resistant through horizontal gene transfer of these plasmids. Selection of a multidrug-resistant Klebsiella pneumoniae strain was also detected following combination antibiotic therapy. Here we report a plasmid carrying the bla_KPC gene with broad host range that poses the additional threat of spreading to endogenous members of the human gut microbiome.IMPORTANCE Antibiotic-resistant bacteria are a serious threat to medically fragile patient populations. The spread of antibiotic resistance through plasmid-mediated mechanisms is of grave concern as it can lead to the conversion of endogenous patient-associated strains to difficult-to-treat pathogens.

Keywords: Enterobacteriaceae; HGT; Klebsiella; antibiotic resistance; carbapenems; genomes; plasmids.

FIG 1

Time line of sequenced isolates, metagenomic samples, and antibiotic courses. Hospitalizations are shown as unfilled boxes (H1 to H8); the HSCT was performed during the first hospitalization. Antibiotic courses are indicated by colored bars; each antibiotic class is shown as a horizontal track. Sequenced isolates are shown at the top and connected by lines. Carbapenemase-producing isolates are shown as filled symbols. Isolates used for plasmid-specific PCR are indicated on the time line as green symbols; all were positive for one or both bla_KPC plasmids. Symbol shape represents the bacterial species: Klebsiella pneumoniae, circles; Klebsiella aerogenes, inverted triangles, Enterobacter cloacae, triangles; Citrobacter freundii, squares. A total of 88 carbapenem-resistant Enterobacteriaceae were collected over 17 months. Metagenomic samples are shown below the hospitalizations as filled diamonds.

FIG 2

Plasmid composition of sequenced Enterobacteriaceae. WGS assemblies were scaffolded onto reference sequences. Plasmids shared across genomes are shown in the same color. The Tn4401b-KPC3 cassette is shown as a magenta circle. Plasmids that are unique to a strain are in black. Plasmids that were detected but could not be scaffolded on an existing reference sequence are shown in gray. The two K. pneunomiae ST340 isolates with chromosomal bla_KPC genes are marked with “^”. Hospitalization number is indicated below each isolate (H1 to H7). Plasmid incompatibility groups were determined using PlasmidFinder v2.0. Plasmid mobility was determined using MOB-suite. Conjugative plasmids are denoted with “(c),” and mobilizable plasmids are marked with “(m).” Nonmobilizable plasmids are unmarked.

FIG 3

Metagenomic read classification of bacteria. Proteobacteria, particularly Enterobacteriaceae, are shown in shades of blue and purple. Relative abundances have been normalized by genome length. Pe, perirectal swab; St, stool. Time points are labeled T1 to T3.