Multispecies Outbreak of Verona Integron-Encoded Metallo-ß-Lactamase-Producing Multidrug Resistant Bacteria Driven by a Promiscuous Incompatibility Group A/C2 Plasmid

Abstract

Background: Antibiotic resistance is often spread through bacterial populations via conjugative plasmids. However, plasmid transfer is not well recognized in clinical settings because of technical limitations, and health care-associated infections are usually caused by clonal transmission of a single pathogen. In 2015, multiple species of carbapenem-resistant Enterobacteriaceae (CRE), all producing a rare carbapenemase, were identified among patients in an intensive care unit. This observation suggested a large, previously unrecognized plasmid transmission chain and prompted our investigation.

Methods: Electronic medical record reviews, infection control observations, and environmental sampling completed the epidemiologic outbreak investigation. A laboratory analysis, conducted on patient and environmental isolates, included long-read whole-genome sequencing to fully elucidate plasmid DNA structures. Bioinformatics analyses were applied to infer plasmid transmission chains and results were subsequently confirmed using plasmid conjugation experiments.

Results: We identified 14 Verona integron-encoded metallo-ß-lactamase (VIM)-producing CRE in 12 patients, and 1 additional isolate was obtained from a patient room sink drain. Whole-genome sequencing identified the horizontal transfer of blaVIM-1, a rare carbapenem resistance mechanism in the United States, via a promiscuous incompatibility group A/C2 plasmid that spread among 5 bacterial species isolated from patients and the environment.

Conclusions: This investigation represents the largest known outbreak of VIM-producing CRE in the United States to date, which comprises numerous bacterial species and strains. We present evidence of in-hospital plasmid transmission, as well as environmental contamination. Our findings demonstrate the potential for 2 types of hospital-acquired infection outbreaks: those due to clonal expansion and those due to the spread of conjugative plasmids encoding antibiotic resistance across species.

Keywords: Enterobacteriaceae; carbapenemase; hospital-acquired infection; plasmid.

Figure 1

A-C. Epidemic curve of VIM-producing CRE by hospital location, organism species, and plasmid variant.

Figure 1

A-C. Epidemic curve of VIM-producing CRE by hospital location, organism species, and plasmid variant.

Figure 1

A-C. Epidemic curve of VIM-producing CRE by hospital location, organism species, and plasmid variant.

Figure 2.

Molecular structure of the In1209 integron identified among all IncA/C2 outbreak plasmids. Resistance genes, except bla_VIM, are in orange.

Figure 3.

A representative for each sub-group of IncA/C2 plasmid. Genes are denoted as arrows. Conjugal transfer genes are depicted in yellow, the bla_VIM gene is in dark blue, the associated In1209 integron is in light blue, the bla_TEM-1B gene and associated mobile elements are purple, the In7 integron is in red, and the In27 integron in green.

Figure 4.

Circular BLAST alignment of all six outbreak IncA/C2 plasmids from PacBio long-read sequencing. White areas indicate absence of a certain genomic region.