Nanopore MinION Sequencing Reveals Possible Transfer of blaKPC–2 Plasmid Across Bacterial Species in Two Healthcare Facilities

Abstract

Carbapenemase-producing Enterobacteriaceae are a major threat to global public health. Klebsiella pneumoniae carbapenemase (KPC) is the most commonly identified carbapenemase in the United States and is frequently found on mobile genetic elements including plasmids, which can be horizontally transmitted between bacteria of the same or different species. Here we describe the results of an epidemiological investigation of KPC-producing bacteria at two healthcare facilities. Using a combination of shortread and long-read whole-genome sequencing, we identified an identical 44 kilobase plasmid carrying the bla KPC−2 gene in four bacterial isolates belonging to three different species (Citrobacter freundii, Klebsiella pneumoniae, and Escherichia coli). The isolates in this investigation were collected from patients who were epidemiologically linked in a region in which KPC was uncommon, suggesting that the antibiotic resistance plasmid was transmitted between these bacterial species. This investigation highlights the importance of long-read sequencing in investigating the relatedness of bacterial plasmids, and in elucidating potential plasmid-mediated outbreaks caused by antibiotic resistant bacteria.

Combining Functional Genomics and Whole-Genome Sequencing to Detect Antibiotic Resistance Genes in Bacterial Strains Co-Occurring Simultaneously in a Brazilian Hospital

“…This might be due to limitations in our draft assemblies. In two recent studies, the authors demonstrated ARG-carrying plasmid transfer in clinical settings between bacteria of the same or different species, emphasizing the significance of revealing potential plasmid-mediated outbreaks to efficiently track horizontal ARG transmission in hospitals [ 44 , 45 ]. Once phages could transfer ARGs among their hosts we also employed Phaster [ 46 ], a web-service for phage identification, to search for the co-occurrence of phages and ARGs, but ARGS were found in phage-related regions of the genomes ( Table S2 ).…”

Escalating antimicrobial resistance among Enterobacteriaceae: focus on carbapenemases

“…KPC-2, the most common CPase in the USA, emerged in North Carolina in 1996 52 , and spread within the USA 53,54 , South America 55 , Europe 30,56 , Israel 57 , South Africa 58 , Asia 1,[59][60][61] , and worldwide 30 . CRE is predominantly due to KPC-2 on plasmids or other MGEs (e.g., insertion sequences, and phage-related sequences) 62,63 . In Brazil, KPC-2 is the most common CPase, carried on plasmids among K. pneumoniae belonging to different international lineages (e.g., sequence type (ST)258, ST101, and ST15) 64 .…”

Combining functional and structural genomics to track antibiotic resistance genes in mobile elements in clinical bacterial strains

“…3 ). In two recent studies, authors demonstrate ARG-carrying plasmids transfer in clinical settings between bacteria of the same or different species, which emphasize the significance of revealing potential plasmid-mediated outbreaks to efficiently track ARGs horizontal transmission in hospitals (30, 31).…”