Article Figures & Data
Figures
- FIG 1
BLAST comparison results for the chromosomes of K. pneumoniae strains PittNDM01 and MGH 78578. A large inversion was identified and verified by PCR in PittNDM01 in comparison with MGH 78578, covering 23.3% of the chromosome.
- FIG 2
Whole-genome phylogeny of K. pneumoniae PittNDM01 relative to other Klebsiella strains. Bootstrap values of ≥50 are shown. The scale bar indicates the distance of 0.04 nucleotide substitutions per site. The tree demonstrates that the core genome of K. pneumoniae PittNDM01 is similar to that of other K. pneumoniae isolates that have been sequenced.
- FIG 3
Overview of pPKPN1. The plasmid carries 12 resistance genes, including blaNDM-1, armA, and qnrB1, which are clustered in two regions of the plasmid containing class 1 integrons. pPKPN1 therefore confers resistance to the three key antimicrobial classes (carbapenems, aminoglycosides, and fluoroquinolones). The numbers indicate the positions on the plasmid.
- FIG 4
Alignment of the blaNDM-1 region of pPKPN1 and representative blaNDM-1-carrying plasmids. The antimicrobial resistance genes and mobile genetic elements are colored in red and brown, respectively. The region surrounding blaNDM-1 differed substantially among the plasmids, with pPKPN1 being especially rich in antimicrobial resistance genes, along with pNDM-CIT.
Tables
- TABLE 1
Overall features of the K. pneumoniae PittNDM01 genome
Parameter Chromosome pPKPN01 pPKPN02 pPKPN03 pPKPN04 Size (bp) 5,348,284 283,371 103,694 70,814 6,141 No. of reads 391,218 19,936 1,505 1,315 99 G+C % 57.50 46.41 51.00 52.92 52.19 No. of predicted open reading frames 4,940 291 101 80 8 Resistance gene(s) blaSHV-28, blaOXA-1, aac(6′)-Ib-cr, cat, macA/macB, fosA blaNDM-1, blaOXA-1, armA, aac(6′)-Ib-cr, aadA2, aphA6, qnrB1, catB4, mel, mph2, dfrA12, sul1 None blaCTX-M-15, blaSHV-11, blaTEM-1, aadA1, aacC2, strB, ereC, cmlA5, sul1, sul2, arr-2 blaOXA-232 - TABLE 2
Detection of methylation in K. pneumoniae PittNDM01
Motifa Modification type No. of motifs detected No. of motifs in genome % motifs detected 5′-GATC-3′ 6mA 63,453 63,698 99.6 3′-CTAG-5′ 5′-CAACNNNNNCGT-3′ 6mA 756 758 99.7 3′-GTTGNNNNNGCA-5′ 756 758 99.7 5′-GATGNNNNNNTTG-3′ 6mA 1,040 1,043 99.7 3′-CTACNNNNNNAAC-5′ 1,037 1,043 99.4 5′-GTCANNNNNNNNTGT-3′ 6mA 322 325 99.1 3′-CAGTNNNNNNNNACA-5′ 324 325 99.7 5′-CCWGG-3′ 5mC 7,296 26,524 27.5 3′-GGWCC-5′ ↵a The methylated positions in the methyltransferase recognition sequence motifs are in bold type.
