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. 2022 Aug 13;12(1):13791.
doi: 10.1038/s41598-022-17996-1.

Genomic epidemiological analysis of Klebsiella pneumoniae from Portuguese hospitals reveals insights into circulating antimicrobial resistance

Anton Spadar  1 , Jody Phelan  1 , Rita Elias  2 , Ana Modesto  2 , Cátia Caneiras  3 , Cátia Marques  4 , Luís Lito  5 , Margarida Pinto  6 , Patrícia Cavaco-Silva  7   8 , Helena Ferreira  9 , Constança Pomba  10 , Gabriela J Da Silva  11 , Maria José Saavedra  12 , José Melo-Cristino  5   13 , Aida Duarte  7   14 , Susana Campino  1 , João Perdigão  2 , Taane G Clark  15   16
Affiliations

Genomic epidemiological analysis of Klebsiella pneumoniae from Portuguese hospitals reveals insights into circulating antimicrobial resistance

Anton Spadar et al. Sci Rep. .

Abstract

Klebsiella pneumoniae (Kp) bacteria are an increasing threat to public health and represent one of the most concerning pathogens involved in life-threatening infections and antimicrobial resistance (AMR). To understand the epidemiology of AMR of Kp in Portugal, we analysed whole genome sequencing, susceptibility testing and other meta data on 509 isolates collected nationwide from 16 hospitals and environmental settings between years 1980 and 2019. Predominant sequence types (STs) included ST15 (n = 161, 32%), ST147 (n = 36, 7%), ST14 (n = 26, 5%) or ST13 (n = 26, 5%), while 31% of isolates belonged to STs with fewer than 10 isolates. AMR testing revealed widespread resistance to aminoglycosides, fluoroquinolones, cephalosporins and carbapenems. The most common carbapenemase gene was blaKPC-3. Whilst the distribution of AMR linked plasmids appears uncorrelated with ST, their frequency has changed over time. Before year 2010, the dominant plasmid group was associated with the extended spectrum beta-lactamase gene blaCTX-M-15, but this group appears to have been displaced by another carrying the blaKPC-3 gene. Co-carriage of blaCTX-M and blaKPC-3 was uncommon. Our results from the largest genomics study of Kp in Portugal highlight the active transmission of strains with AMR genes and provide a baseline set of variants for future resistance monitoring and epidemiological studies.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Phylogenetic trees of the most commons sequence types (STs), their antimicrobial resistance (AMR) phenotype, and carbapenemase and ESBL genotypic profiles. K-Loci refer to inferred K serotypes. Branch colours represent bootstrap support values.
Figure 1
Figure 1
Phylogenetic trees of the most commons sequence types (STs), their antimicrobial resistance (AMR) phenotype, and carbapenemase and ESBL genotypic profiles. K-Loci refer to inferred K serotypes. Branch colours represent bootstrap support values.
Figure 2
Figure 2
The most common ESBL (blaCTX-M-15) and carbapenemase (blaKPC-3) genes across the 509 Kp isolates by year group.
Figure 3
Figure 3
(A) Clustering of isolates by their plasmid replicon (replicon clusters, RC) and antimicrobial resistance (AMR) genotypic profiles, revealing differentiation by carriage of blaKPC-3 and blaCTX-M-15 genes. X and Y axis are dimensions on which full data is projected, they are unitless; (B) Abundance of isolates from different plasmid clusters.
Figure 4
Figure 4
Distribution of inhibition zone diameters for different genotypes for (A) imipenem, (B) cefotaxime, (C) cefoxitin, (D) ciproflocaxin, and (E) gentamicin antimicrobials.
See this image and copyright information in PMC

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