Research Article | Clinical Science and Epidemiology

Horizontal Plasmid Transfer among Klebsiella pneumoniae Isolates Is the Key Factor for Dissemination of Extended-Spectrum β-Lactamases among Children in Tanzania

Torunn Pedersen, Marit Gjerde Tellevik, Øyvind Kommedal, Paul Christoffer Lindemann, Sabrina John Moyo, Jessin Janice, Bjørn Blomberg, Ørjan Samuelsen, Nina Langeland
Mariana Castanheira, Editor
DOI: 10.1128/mSphere.00428-20

Article Figures & Data

Figures

  • FIG 1
    FIG 1

    Phylogenetic tree of CTX-M-15-encoding K. pneumoniae (n = 128) revealed by rapid core genome multialignment (https://github.com/marbl/parsnp). Metadata, including location of patient residence, source of isolation and time of sample collection within the 12-month study period (increased darkness of color), and group of plasmid, are visualized for each strain in the concentric rings (color codes as shown). Strains selected for long-read DNA sequencing are marked in bold. The tree is midpoint rooted with scale as shown.

  • FIG 2
    FIG 2

    K. pneumoniae global phylogeny revealed by rapid core genome multialignment (https://github.com/marbl/parsnp). Assembly data set from this study (n = 128; red) were analyzed together with data sets from the PATRIC database (n = 970), for which GenBank assembly accession numbers are given for each of the PATRIC strains.

  • FIG 3
    FIG 3

    DNA alignment of blaCTX-M-15-containing plasmids. The concentric circles represent BLAST comparisons of plasmids pK020_1 (green) and pK006_3, pK033_1, and pK039_2 (dark blue) against the pK012_2 reference (red). The annotated coding DNA sequence (CDS) of the reference plasmid is shown in the outer circle, with the replication initiation encoding genes (gray), resistance-encoding genes (purple), IS elements (black), and F-conjugation module genes (light blue) highlighted. Color codes for DNA identity ranging from 100% to 50% as indicated. The map was constructed using the BLAST Ring Image Generator (http://brig.sourceforge.net/).

  • FIG 4
    FIG 4

    Tracking of CTX-M-15-encoding plasmid sequences by using pK020_1 as a reference. The green concentric circles (n = 37) represent BLAST comparisons of the genome assemblies (strains listed) against the reference, starting with the innermost circle. Color codes for strains belonging to STs which include three or more strains, and for DNA identity ranging from 100% to 50% identity, are indicated. The red circles represent the reference, including annotated CDS in which replication initiation encoding genes (gray), resistance-encoding genes (purple), and IS elements (black) are highlighted.

  • FIG 5

    Tracking of CTX-M-15-encoding plasmid sequences by using pK012_2 as a reference. The blue concentric circles (n = 90) represent BLAST comparisons of the genome assemblies against the reference plasmid, starting with the first of the listed strains as the innermost circle. Color codes for DNA identity ranging from 100% to 50% are indicated. The red circles represent the reference, including annotated CDS in which replication initiation-encoding genes (gray), resistance-encoding genes (purple), IS elements (black), and F-conjugation module genes (light blue) are highlighted.

  • FIG 6
    FIG 6

    Comparison of pK012_2 with completed plasmids from the NCBI reference database. The concentric multicolored circles represent BLAST comparisons of selected plasmids having an overall coverage of >50% and DNA identity of >97% (n = 24; color codes as indicated) correlated to pK012_2. Accession numbers and color codes for each of the plasmids are given. The red circles represent the pK012_2 reference plasmid, including annotated CDS in which replication initiation-encoding genes (gray), resistance-encoding genes (purple), IS elements (black), and F-conjugation module genes (light blue) are highlighted.

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KEYWORDS

CTX-M-15
HGT
IncFIIK5 plasmid
Klebsiella pneumoniae
whole-genome sequencing

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