Distinguishing blaKPC Gene-Containing IncF Plasmids from Epidemiologically Related and Unrelated Enterobacteriaceae Based on Short- and Long-Read Sequence Data

Joep J J M Stohr; Marjolein F Q Kluytmans-van den Bergh; Veronica A T C Weterings; John W A Rossen; Jan A J W Kluytmans

doi:10.1128/AAC.00147-21

Distinguishing bla_KPC Gene-Containing IncF Plasmids from Epidemiologically Related and Unrelated Enterobacteriaceae Based on Short- and Long-Read Sequence Data

Antimicrob Agents Chemother. 2021 May 18;65(6):e00147-21. doi: 10.1128/AAC.00147-21. Print 2021 May 18.

Authors

Joep J J M Stohr^{1

2}, Marjolein F Q Kluytmans-van den Bergh^{3

4

5}, Veronica A T C Weterings³, John W A Rossen^{6

7}, Jan A J W Kluytmans^{3

2

4

5}

Affiliations

¹ Department of Infection Control, Amphia Hospital, Breda, the Netherlands joep.stohr@gmail.com.
² Laboratory for Medical Microbiology and Immunology, Elisabeth-TweeSteden Hospital, Tilburg, the Netherlands.
³ Department of Infection Control, Amphia Hospital, Breda, the Netherlands.
⁴ Amphia Academy Infectious Disease Foundation, Amphia Hospital, Breda, the Netherlands.
⁵ Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.
⁶ Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
⁷ Department of Pathology, University of Utah, School of Medicine, Salt Lake City, Utah, USA.

Abstract

Limited information is available on whether bla_KPC-containing plasmids from isolates in a hospital outbreak can be differentiated from epidemiologically unrelated bla_KPC-containing plasmids based on sequence data. This study aimed to evaluate the performance of three approaches to distinguish epidemiologically related from unrelated bla_KPC-containing pKpQiL-like IncFII(k2)-IncFIB(pQiL) plasmids. Epidemiologically related isolates were subjected to short- and long-read whole-genome sequencing. A hybrid assembly was performed, and plasmid sequences were extracted from the assembly graph. Epidemiologically unrelated plasmid sequences were extracted from GenBank. Pairwise comparisons of epidemiologically related and unrelated plasmids based on SNPs using snippy and of phylogenetic distance using Roary and using a similarity index that penalizes size differences between plasmids (Stoesser index) were performed. The percentage of pairwise comparisons misclassified as genetically related or as clonally unrelated was determined using different genetic thresholds for genetic relatedness. The ranges of number of SNPs, Roary phylogenetic distance, and Stoesser index overlapped between the epidemiologically related and unrelated plasmids. When a genetic similarity threshold that classified 100% of epidemiologically related plasmid pairs as genetically related was used, the percentages of plasmids misclassified as epidemiologically related ranged from 6.7% (Roary) to 20.8% (Stoesser index). Although epidemiologically related plasmids can be distinguished from unrelated plasmids based on genetic differences, bla_KPC-containing pKpQiL-like IncFII(k2)-IncFIB(pQiL) plasmids show a high degree of sequence similarity. The phylogenetic distance as determined using Roary showed the highest degree of discriminatory power between the epidemiologically related and unrelated plasmids.

Keywords: KPC; plasmids; transmission.

MeSH terms

Bacterial Proteins / genetics
Enterobacteriaceae* / genetics
Klebsiella pneumoniae / genetics
Phylogeny
Plasmids / genetics
beta-Lactamases* / genetics

Substances

Bacterial Proteins
beta-Lactamases