New preprint: using genetics to analyse ESBL infections in a neonatal ICU ward

In this preprint, Melody Parker as part of her DPhil, has analysed a series of infections in a neonatal intensive care unit. At the time there was concern that this could be an outbreak; if so the ICU team would want to improve their infection control measures. Whole genome sequencing can give you the really fine-grained resolution to be able to say that these two infections likely came from the same source or, more subtly for Enterobacterales, that the plasmid carrying the AMR gene in these two different species is identical and therefore is likely to have hopped from one to the other in the hospital environment.

Answering these questions is a challenge and required Melody to compare both the chromosomes of the different bacteria in the samples as well as the plasmids. The latter are especially tricky due to how they can shuffle genetic material around, hence she had to use the number of double-cut and joins (measured using pling) as a measure of how similar different plasmids in a community were.

She found no evidence of plasmids containing bla_CTX-M alleles moving between species and the data suggested the increase in infections was driven by several small outbreaks of different strains introduced to the ICU from outside.