The detection of KPC-2, NDM-1, and VIM-2 carbapenemases in international clones isolated from fresh vegetables highlights an emerging food safety issue

• Published in: International journal of food microbiology Vol. 420; p. 110765
• Main Authors: Furlan, João Pedro Rueda, Lopes, Ralf, Ramos, Micaela Santana, Rosa, Rafael da Silva, dos Santos, Lucas David Rodrigues, Stehling, Eliana Guedes
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 02-08-2024
• Subjects: Anti-Bacterial Agents - pharmacology; Antimicrobial resistance; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; beta-Lactamases - genetics; beta-Lactamases - metabolism; Carbapenemase; Drug Resistance, Multiple, Bacterial - genetics; Escherichia coli; Escherichia coli - drug effects; Escherichia coli - enzymology; Escherichia coli - genetics; Escherichia coli - isolation & purification; Food Microbiology; Food Safety; Humans; Klebsiella pneumoniae; Klebsiella pneumoniae - drug effects; Klebsiella pneumoniae - enzymology; Klebsiella pneumoniae - genetics; Klebsiella pneumoniae - isolation & purification; Microbial Sensitivity Tests; Plasmid; Plasmids - genetics; Pseudomonas aeruginosa; Pseudomonas aeruginosa - drug effects; Pseudomonas aeruginosa - enzymology; Pseudomonas aeruginosa - genetics; Pseudomonas aeruginosa - isolation & purification; Vegetables - microbiology; Whole Genome Sequencing; Plasmid; Carbapenemase; Pseudomonas aeruginosa; Antimicrobial resistance; Escherichia coli; Klebsiella pneumoniae
• ISSN: 0168-1605; 1879-3460; 1879-3460
• DOI: 10.1016/j.ijfoodmicro.2024.110765

Resistance to carbapenems emerged in clinical settings and has rapidly spread to other sectors, such as food and the environment, representing a One Health problem. In this regard, vegetables contaminated by critical priority pathogens have raised global concerns. Here, we have performed a whole-genome sequence-based analysis of extensively drug-resistant Klebsiella pneumoniae, Escherichia coli, and Pseudomonas aeruginosa strains isolated from cabbage, spinach, and lettuce, respectively. Genomic analysis revealed the emergence of international and high-risk clones belonging to ST340, ST155, and ST233, harboring a broad resistome to clinically important antimicrobials. In this context, K. pneumoniae, E. coli, and P. aeruginosa strains carried blaKPC-2, blaNDM-1, and blaVIM-2, respectively. The blaKPC-2 gene with a non-Tn4401 element (NTEKPC-Ic) was located on an IncX3-IncU plasmid, while the blaVIM-2 gene was associated with a Tn402-like class 1 integron, In559, on the chromosome. Curiously, the blaNDM-1 gene coexisted with the blaPER-2 gene on an IncC plasmid and the regions harboring both genes contained sequences of Tn3-like element ISKox2-like family transposase. Comparative genomic analysis showed interspecies and clonal transmission of carbapenemase-encoding genes at the human-animal-environmental interface. These findings raise a food safety alert about hospital-associated carbapenemase producers, supporting that fresh vegetables can act as a vehicle for the spread of high-risk clones.
•Extensively drug-resistant K. pneumoniae, E. coli, and P. aeruginosa strains were isolated from vegetables.•The international clones ST340, ST155, and ST233 carried different carbapenamase-encoding genes.•The blaKPC-2 and blaNDM-1 were located on plasmids, while blaVIM-2 was integrated into the chromosome.•Interspecies and clonal transmission of carbapenemases-encoding genes have been demonstrated.