The Emerging Nosocomial Pathogen Klebsiella michiganensis : Genetic Analysis of a KPC-3 Producing Strain Isolated from Venus Clam

• Published in: Microbiology spectrum Vol. 11; no. 1; p. e0423522
• Main Authors: Simoni, Serena, Leoni, Francesca, Veschetti, Laura, Malerba, Giovanni, Carelli, Maria, Lleò, Maria M, Brenciani, Andrea, Morroni, Gianluca, Giovanetti, Eleonora, Rocchegiani, Elena, Barchiesi, Francesca, Vignaroli, Carla
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 14.02.2023
• Subjects: Anti-Bacterial Agents - pharmacology; Antimicrobial Chemotherapy; Bacterial Proteins - genetics; beta-Lactamases - genetics; carbapenem-resistance; Carbapenems - pharmacology; Cross Infection; Drug Resistance, Multiple, Bacterial - genetics; Hospitals; Humans; Klebsiella Infections - epidemiology; Klebsiella michiganensis; Klebsiella pneumoniae; KPC-3; Microbial Sensitivity Tests; Phylogeny; pKpQIL plasmids; Plasmids - genetics; Research Article; KPC-3; Klebsiella michiganensis; carbapenem-resistance; pKpQIL plasmids
• ISSN: 2165-0497; 2165-0497
• DOI: 10.1128/spectrum.04235-22

The recovery and characterization of a multidrug-resistant, KPC-3-producing Klebsiella michiganensis that was obtained from Venus clam samples is reported in this study. A whole-genome sequencing (WGS) analysis using Illumina and Nanopore technologies of the 23999A2 isolate revealed that the strain belonged to the new sequence type 382 (ST382) and carried seven plasmid replicon sequences, including four IncF type plasmids (FII, FIIY, FIIk, and FIB), one IncHI1 plasmid, and two Col plasmids. The FIB and FII plasmids showed high homology to each other and to multireplicon pKpQIL-like plasmids that are found in epidemic KPC-K. pneumoniae clones worldwide. The strain carried multiple β-lactamase genes on the IncF plasmids: and on FIB, inserted in a Tn on FII , and on FII . The IncHI1-ST11 harbored no resistance gene. The curing of the strain caused the loss of all of the genes and a rearrangement of the IncF plasmids. Conjugal transfer of the , and genes occurred at a frequency of 5 × 10 , using as a recipient, and all of the genes were transferred through a pKpQIL that originated from the recombination of the FIB and FIIk plasmids of the donor. A comparison with 31 genomes that are available in the NCBI database showed that the closest phylogenetic relatives of 23999A2 are an environmental isolate from soil in South Korea and a clinical isolate from human sputum in Japan. Finally, a pan-genome analysis showed a large accessory genome of the strain as well as the great genomic plasticity of the species. Klebsiella michiganensis is an emerging nosocomial pathogen, and, so far, few studies describe isolates of clinical origin in the environment. This study contributes to the understanding of how the dissemination of carbapenem-resistance outside the hospital setting may be related to the circulation of pKpQIL-like plasmids that are derived from epidemic Klebsiella pneumoniae strains. The recovery of a carbapenem-resistant isolate in clams is of great concern, as bivalves could represent vehicles of transmission of pathogens and resistance genes to humans via the food chain. The study demonstrates the plasticity of genome, which is probably useful to multiple environment adaptation and to the evolution of the species.