Genetic plurality of blaKPC-2-harboring plasmids in high-risk clones of Klebsiella pneumoniae of environmental origin

• Published in: The Science of the total environment Vol. 881; p. 163322
• Main Authors: Furlan, João Pedro Rueda, da Silva Rosa, Rafael, Ramos, Micaela Santana, dos Santos, Lucas David Rodrigues, Lopes, Ralf, Savazzi, Eduardo Angelino, Stehling, Eliana Guedes
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 10-07-2023
• Subjects: Antimicrobial resistance; Critical-priority pathogen; Environmental contamination; One Health; Plasmidome; Environmental contamination; Plasmidome; Antimicrobial resistance; Critical-priority pathogen; One Health
• ISSN: 0048-9697; 1879-1026
• DOI: 10.1016/j.scitotenv.2023.163322

International high-risk clones of Klebsiella pneumoniae are important human pathogens that are spreading to the environment. In the COVID-19 pandemic scenario, the frequency of carbapenemase-producing strains increased, which can contribute to the contamination of the environment, impacting the surrounding and associated ecosystems. In this regard, KPC-producing strains were recovered from aquatic ecosystems located in commercial, industrial, or agricultural areas and were submitted to whole-genome characterization. K. pneumoniae and Klebsiella quasipneumoniae subsp. quasipneumoniae strains were assigned to high-risk clones (ST11, ST340, ST307) and the new ST6325. Virulome analysis showed genes related to putative hypervirulence. Strains were resistant to almost all antimicrobials tested, being classified as extensively drug-resistant or multidrug-resistant. In this context, a broad resistome (clinically important antimicrobials and hazardous metal) was detected. Single replicon (IncX5, IncN-pST15, IncU) and multireplicon [IncFII(K1)/IncFIB(pQil), IncFIA(HI1)/IncR] plasmids were identified carrying the blaKPC-2 gene with Tn4401 and non-Tn4401 elements. An unusual association of blaKPC-2 and qnrVC1 and the coexistence of blaKPC-2 and mer operon (mercury tolerance) was found. Comparative analysis revealed that blaKPC-2-bearing plasmids were most similar to plasmids from Enterobacterales of Brazil, China, and the United States, evidencing the long persistence of plasmids at the human-animal-environmental interface. Furthermore, the presence of uncommon plasmids, displaying the interspecies, intraspecies, and clonal transmission, was highlighted. These findings alert for the spread of high-risk clones producing blaKPC-2 in the environmental sector and call attention to rapid dispersion in a post-pandemic world.
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•Dispersion of XDR or MDR high-risk clones was observed in aquatic ecosystems.•The coexistence of blaKPC-2 and mer operon (mercury tolerance) was found.•Diversity of single and multireplicon plasmids bearing the blaKPC-2 gene was identified.•Comparative analysis revealed interspecies, intraspecies, and clonal transmission.•The long persistence of plasmids at the human-animal-environmental interface is discussed.