| Literature DB >> 24961694 |
Liang Chen1, Barun Mathema, Johann D D Pitout, Frank R DeLeo2, Barry N Kreiswirth3.
Abstract
UNLABELLED: Carbapenem-resistant Enterobacteriaceae (CRE), especially Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae, pose an urgent threat in health facilities in the United States and worldwide. K. pneumoniae isolates classified as sequence type 258 (ST258) by multilocus sequence typing are largely responsible for the global spread of KPC. A recent comparative genome study revealed that ST258 K. pneumoniae strains are two distinct genetic clades; however, the molecular origin of ST258 largely remains unknown, and our understanding of the evolution of the two genetic clades is incomplete. Here we compared the genetic structures and single-nucleotide polymorphism (SNP) distributions in the core genomes of strains from two ST258 clades and other STs (ST11, ST442, and ST42). We identified an ~1.1-Mbp region on ST258 genomes that is homogeneous to that of ST442, while the rest of the ST258 genome resembles that of ST11. Our results suggest ST258 is a hybrid clone--80% of the genome originated from ST11-like strains and 20% from ST442-like strains. Meanwhile, we sequenced an ST42 strain that carries the same K-antigen-encoding capsule polysaccharide biosynthesis gene (cps) region as ST258 clade I strains. Comparison of the cps-harboring regions between the ST42 and ST258 strains (clades I and II) suggests the ST258 clade I strains evolved from a clade II strain as a result of cps region replacement. Our findings unravel the molecular evolution history of ST258 strains, an important first step toward the development of diagnostic, therapeutic, and vaccine strategies to combat infections caused by multidrug-resistant K. pneumoniae. IMPORTANCE: Recombination events and replacement of chromosomal regions have been documented in various bacteria, and these events have given rise to successful pathogenic clones. Here we used comparative genomic analyses to discover that the ST258 K. pneumoniae genome is a hybrid--80% of the chromosome is homologous to ST11 strains, while the remaining 20% is homologous to that of ST442. Meanwhile, a recent study indicated that ST258 strains can be segregated into two ST258 clades, with distinct capsule polysaccharide gene (cps) regions. Our analysis suggests ST258 clade I strains evolved from clade II through homologous recombination of cps region. Horizontal transfer of the cps region appears to be a key element driving the molecular diversification in K. pneumoniae strains. These findings not only extend our understanding of the molecular evolution of ST258 but are an important step toward the development of effective control and treatment strategies for multidrug-resistant K. pneumoniae.Entities:
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Year: 2014 PMID: 24961694 PMCID: PMC4073492 DOI: 10.1128/mBio.01355-14
Source DB: PubMed Journal: mBio Impact factor: 7.867
Features of completely sequenced ST258, ST11, and ST442 genomes
| Parameter[ | Result for strain: | |||||
|---|---|---|---|---|---|---|
| NJST258_1 | NJST258_2 | HS11286 | JM45 | ATCC BAA-2146 | Kp13 | |
| ST no. | 258 | 258 | 11 | 11 | 11 | 442 |
| Yr | 2010 | 2010 | 2011 | 2010 | 2010 | 2009 |
| Country | United States | United States | China | China | United States | Brazil |
| Size (bp) | 5,263,329 | 5,293,301 | 5,333,942 | 5,273,813 | 5,435,369 | 5,307,003 |
| 57.4 | 57.5 | 57.5 | 57.5 | 57.3 | 57.5 | |
| No. of CDS | 5,475 | 5,434 | 5,316 | 4,872 | 5,315 | 5,189 |
| rRNA ( | 25 | 25 | 25 | 25 | 25 | 24 |
| 16S | 8 | 8 | 8 | 8 | 8 | 8 |
| 23S | 8 | 8 | 8 | 8 | 8 | 8 |
| 5S | 9 | 9 | 9 | 9 | 9 | 8 |
| tRNA ( | 77 | 86 | 87 | 83 | 85 | 86 |
| Plasmids ( | 5 | 3 | 6 | 2 | 4 | 6 |
| Prophages ( | 8 | 7 | 7 | 7 | 8 | 2 |
| ICEs ( | 2 | 2 | 2 | 1 | 3 | 1 |
| IS elements ( | 22 | 19 | 23 | 14 | 23 | 31 |
| IS family ( | IS | IS | IS | IS | IS | IS |
ICE, integrated conjugative element; IS, insertion sequence; CDS, coding sequences.
FIG 1 (A) MLST allele locations on NJST258_1 genome. The light green arrow denotes the genome of NJST258_1, and the light blue region shows the ~1.1-Mbp putative recombination region between the ST11 and ST442 genomes. The chromosomal positions of the seven MLST housekeeping genes (gapA, infB, mdh, pgi, phoE, rpoB, and tonB) are illustrated beneath the genome arrow of NJST258_1, and the corresponding allele numbers for ST11, ST258, ST442, and ST42 are listed below the gene names. (B) Core genome SNP distributions in the ST11, ST258 (clades I and II), ST442, and ST42 strains. The number of SNPs (y axis) per 1,000 nt is plotted according to the position on the NJST258_1 genome (x axis). Different homogeneous regions (>98% identity based on SNP comparisons) are color coded. Specifically, the ~52-kb cps-containing regions in Kp1787 (ST258 clade I) and Kp1832 (ST42), which are nearly identical in these strains, are shaded in green. ICEKp258.2 and cps are illustrated by small vertical bars, and the same cps regions are shown in the same color.
FIG 2 Upstream and downstream junction SNPs for the ~1.1-Mbp recombination fragment and cps region in ST258, ST442, and ST42 strains. The start site of the replacement of the ~52-kb cps-harboring region is the same as that of the ~215-kb RD in ST258 II clades (7). Sequences were obtained from Kp1878 (an ST258 clade I strain), NJST258_1 (an ST258 clade II strain), JM45 (an ST11 strain), Kp1832 (an ST42 strain), and Kp13 (an ST442 strain).
FIG 3 (A) SNP matrix for different K. pneumonaie strains. The matrix is illustrated as (total no. of SNPs/no. of SNPs in the ~1.1-Mbp recombination region). Green shading indicates the number of SNPs in ST258 strains compared to that in ST11 strains. Orange shading indicates the number of SNPs in ST258 strains compared to that in ST442 strains. (B) Phylogenetic analysis of the eight isolates based upon 52,135 concatenated SNPs in the core genome.
FIG 4 Hypothesized evolutionary history in K. pneumoniae ST258 strains.