Comparative genomics of IncQ1 plasmids carrying bla GES variants from clinical and environmental sources in Brazil

• Published in: Infection, genetics and evolution Vol. 123; p. 105644
• Main Authors: Conte, Danieli, Mesa, Dany, Krul, Damaris, Bail, Larissa, Ito, Carmen Antônia Sanches, Palmeiro, Jussara Kasuko, Dalla-Costa, Libera Maria
• Format: Journal Article
• Language: English
• Published: Netherlands 01.09.2024
• Subjects: Aeromonas - drug effects; Aeromonas - genetics; Aeromonas - isolation & purification; Anti-Bacterial Agents - pharmacology; beta-Lactamases - genetics; Brazil; Genome, Bacterial; Genomics - methods; Humans; Integrons - genetics; Klebsiella - drug effects; Klebsiella - genetics; Microbial Sensitivity Tests; Plasmids - genetics; Whole Genome Sequencing; Brazil; GES enzymes; Aeromonas veronii; Klebsiella variicola; Class 1 integron; Antibiotic resistance genes

IncQ-type plasmids have become important vectors in the dissemination of bla among different bacterial genera and species from different environments around the world, and studies estimating the occurrence of Guiana extended-spectrum (GES)-type β-lactamases are gaining prominence. We analyzed the genetic aspects of two IncQ1 plasmids harboring different bla variants from human and environmental sources. The bla variants were identified using polymerase chain reaction (PCR) in Aeromonas veronii isolated from hospital effluent and Klebsiella variicola isolated from a rectal swab of a patient admitted to the cardiovascular intensive care unit in a different hospital. Antimicrobial-susceptibility testing and transformation experiments were performed for phenotypic analysis. Whole-genome sequencing was performed using Illumina and Oxford Nanopore platforms. The comparative analysis of plasmids was performed using BLASTn, and the IncQ1 plasmids showed a high identity and similar size. A. veronii harbored bla in a class 1 integron (In2061), recently described by our group, and K. variicola carried bla in the known class 1 integron. Both integrons showed a fused gene cassette that encodes resistance to aminoglycosides and fluoroquinolones, with an IS6100 truncating the 3'-conserved segment. The fused genes are transcribed together, although the attC site is disrupted. These gene cassettes can no longer be mobilized. This study revealed a mobilome that may contribute to the dissemination of GES-type β-lactamases in Brazil. Class 1 integrons are hot spots for bacterial evolution, and their insertion into small IncQ-like plasmids displayed successful recombination, allowing the spread of bla variants in various environments. Therefore, they can become prevalent across clinically relevant pathogens.