Utility of hybrid whole genome sequencing in assessing potential nosocomial VIM transmission

Abstract

Hybrid whole genome sequencing was used to investigate if nosocomial Verona integron-encoded metallo-β-lactamase (VIM) carbapenemase transmission occurred between two patients without epidemiological links or common pathogens. Challenges in genomic methodology and appropriate analytical depth for mobile carbapenemase outbreaks are described including how inappropriate choices can mislead results and impact infection control practices.

Figure 1.

Overview of mobile VIM genomic analysis results. A The annotated VIM-bearing plasmids assembled from each of the isolates. The VIM gene is highlighted in orange and identified integrons in the plasmids marked using a dark gray bar in the inner circle. B The alignment and comparison of the three VIM-bearing integrons. The vertical ribbons indicate genes with shared sequence identity between the integrons (as per the % identity scale bar). C A comparison of the VIM alleles in each taxa in the form of a truncated alignment showing all the sequence differences.

Figure 2.

An overview of analyses and conflicting results during the investigation of a possible nosocomial transmission of a mobile VIM carbapenemase. Ticks and crosses (and associated box highlighting), respectively, represent information that supported or refuted potential linkage between patients.