Complexity of Genomic Epidemiology of Carbapenem-Resistant Klebsiella pneumoniae Isolates in Colombia Urges the Reinforcement of Whole Genome Sequencing-Based Surveillance Programs

Abstract

Background: Carbapenem-resistant Klebsiella pneumoniae (CRKP) is an emerging public health problem. This study explores the specifics of CRKP epidemiology in Colombia based on whole genome sequencing (WGS) of the National Reference Laboratory at Instituto Nacional de Salud (INS)'s 2013-2017 sample collection.

Methods: A total of 425 CRKP isolates from 21 departments were analyzed by HiSeq-X10®Illumina high-throughput sequencing. Bioinformatic analysis was performed, primarily using the pipelines developed collaboratively by the National Institute for Health Research Global Health Research Unit (GHRU) on Genomic Surveillance of Antimicrobial Resistance (AMR), and AGROSAVIA.

Results: Of the 425 CRKP isolates, 91.5% were carbapenemase-producing strains. The data support a recent expansion and the endemicity of CRKP in Colombia with the circulation of 7 high-risk clones, the most frequent being CG258 (48.39% of isolates). We identified genes encoding carbapenemases blaKPC-3, blaKPC-2, blaNDM-1, blaNDM-9, blaVIM-2, blaVIM-4, and blaVIM-24, and various mobile genetic elements (MGE). The virulence of CRKP isolates was low, but colibactin (clb3) was present in 25.2% of isolates, and a hypervirulent CRKP clone (CG380) was reported for the first time in Colombia. ST258, ST512, and ST4851 were characterized by low levels of diversity in the core genome (ANI > 99.9%).

Conclusions: The study outlines complex CRKP epidemiology in Colombia. CG258 expanded clonally and carries specific carbapenemases in specific MGEs, while the other high-risk clones (CG147, CG307, and CG152) present a more diverse complement of carbapenemases. The specifics of the Colombian situation stress the importance of WGS-based surveillance to monitor evolutionary trends of sequence types (STs), MGE, and resistance and virulence genes.

Keywords: Klebsiella pneumoniae; Carbapenemases; antimicrobial resistance; whole genome sequence (WGS).

Figure 1.

Geographical distribution of mechanisms of resistance to carbapenems in Klebsiella pneumoniae and core genome tree in Colombia, 2013–2017. a) Map depicting the 21 departments that submitted isolates for surveillance. Isolates were classified according to the mechanism of resistance to carbapenem by color (see key). Pie chart shows the proportions of different mechanisms of resistance to carbapenems in each department. b) Circular representation of the transformed phylogenetic tree showing the genetic relationships among 421 Colombian K. pneumoniae CRKP isolates. Phylogenetic tree was built using 421/425 isolates; 4 were excluded from the analysis because they presented a high number of N in the multiple alignments. The 421 isolates were classified into 80 STs grouped in 42 CG and 9 singletons. Due to the number of different CGs, for the graph, CGs with ≥6 isolates were selected for easy viewing on the tree: CG258, CG13, CG14/15, CG17/20, CG25, CG39, CG45, CG70, CG76, CG147, CG152, and CG307. Remaining CG and singletons were classified as other-CG. Abbreviations: CG, clonal group; CRKP, carbapenem-resistant Klebsiella pneumoniae; ST. sequence type.

Figure 2.

Clonal group heat maps, virulence factors, resistance profile, carbapenemases, replicons, and alluvial of the CG258. Heatmap analyzes different clonal groups (each row of the heatmap represents a clonal group). a) Heatmap displaying the distribution of antimicrobials and the mechanism of resistance to carbapenems (y-axis) in the clonal group. b) Heatmap displaying the distribution of O locus, K locus (wzi), and virulence factors (y-axis) found in the clonal group. c) Heatmap displaying the distribution of the replicon type (y-axis) found in the clonal group. d) Alluvial diagram showing the “flow” of the presence of the most important transposable elements associated with carbapenemase and ST of CG258. Abbreviation: ST, sequence type.