Molecular epidemiology of Klebsiella variicola obtained from different sources

Abstract

Klebsiella variicola is considered an emerging pathogen in humans and has been described in different environments. K. variicola belongs to Klebsiella pneumoniae complex, which has expanded the taxonomic classification and hindered epidemiological and evolutionary studies. The present work describes the molecular epidemiology of K. variicola based on MultiLocus Sequence Typing (MLST) developed for this purpose. In total, 226 genomes obtained from public data bases and 28 isolates were evaluated, which were mainly obtained from humans, followed by plants, various animals, the environment and insects. A total 166 distinct sequence types (STs) were identified, with 39 STs comprising at least two isolates. The molecular epidemiology of K. variicola showed a global distribution for some STs was observed, and in some cases, isolates obtained from different sources belong to the same ST. Several examples of isolates corresponding to kingdom-crossing bacteria from plants to humans were identified, establishing this as a possible route of transmission. goeBURST analysis identified Clonal Complex 1 (CC1) as the clone with the greatest distribution. Whole-genome sequencing of K. variicola isolates revealed extended-spectrum β-lactamase- and carbapenemase-producing strains with an increase in pathogenicity. MLST of K. variicola is a strong molecular epidemiological tool that allows following the evolution of this bacterial species obtained from different environments.

Figure 1

Molecular epidemiology of K. variicola isolates. The map shows the localization of each ST. The underlined ST corresponds to ST with two or more isolates. The major ST corresponds to genomes described in the USA, Mexico, Germany and China. The origin of the isolates is shown in color codes. The ST market with asterisks corresponds to K. variicola outbreaks. The WGS projects of Klebsiella in the USA are marked with a diamond, corresponding to Texas and Missouri. The black circles in Europe correspond to countries described with a single or two ST (ST underline), as: Greece (ST86), Austria ST125, Belgium (ST132), Estonia (ST139), Croatia (ST142 and ST143), Hungary (ST144), Poland (ST156), Serbia (ST160) and Slovenia (ST161 and ST162).

Figure 2

goeBURST analysis of K. variicola isolates. Single-locus variants (SLVs) are in red, double-locus variants (DLVs) are in black, and triple-locus variants (TLVs) are in grey. The founder ST10 and ST38, ST23 and ST130 with an SLV correspond to Clonal Complex 1 (CC1). The isolates from humans and plants are in green and orange squares, respectively. The size of a node is proportional to the number of isolates presenting that ST in the database (Supplementary Dataset).

Figure 3

Phylogenetic tree of K. variicola isolates obtained from different sources. The tree includes the seven concatenated genes from genomes and the isolates described in the present study. Isolates associated with human infection are indicated by white circles, endophyte and rhizosphere isolates with black circles, isolates obtained from animals with black square, insect isolates with black diamond, environmental isolates with black triangles and isolates with unknown or missing origin with white squares. ESBL- and carbapenemase-producing isolates are represented by blue and red circles, respectively. KCB corresponds to kingdom-crossing bacteria identified in the analysis.

Figure 4

Molecular epidemiology of ESBL- and carbapenemase-producing K. variicola isolates. Underlined STs contain several isolates. ST and ESBL- and/or carbapenemase-producing genes corresponding to K. variicola outbreaks are marked with asterisks. The origin of the isolates is shown in color codes. The IMI-2 and OXA-181 carbapenemase-producing K. variicola isolates lack WGS data.

Figure 5

Timeline description of K. variicola isolates and genomes described in public databases. The KpIII group corresponds to K. variicola. The K. variicola pediatric outbreak marked with asterisk corresponds to the isolation date of the clinical isolates.