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Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are diverse immune systems found in many prokaryotic genomes that target invading foreign DNA such as bacteriophages and plasmids. There are multiple types of CRISPR with arguably the most enigmatic being Type IV. During an investigation of CRISPR carriage in clinical, multi-drug resistant,  Klebsiella pneumoniae , a Type IV-A3 CRISPR-Cas system was detected on plasmids from two  K. pneumoniae  isolates from Egypt (isolated in 2002–2003) and a single  K. pneumoniae  isolate from the United Kingdom (isolated in 2017). Sequence analysis of all other genomes available in GenBank revealed that this CRISPR-Cas system was present on 28 other plasmids from various  Enterobacteriaceae  hosts and was never found on a bacterial chromosome. This system is exclusively located on  IncHI1B/IncFIB  plasmids and is associated with multiple putative transposable elements. Expression of the  cas  loci was confirmed in the available clinical isolates by RT-PCR. In all cases, the CRISPR-Cas system has a single CRISPR array (CRISPR1) upstream of the  cas  loci which has several, conserved, spacers which, amongst things, match regions within conjugal transfer genes of  IncFIIK/IncFIB(K)  plasmids. Our results reveal a Type IV-A3 CRISPR-Cas system exclusively located on  IncHI1B/IncFIB  plasmids in  Enterobacteriaceae  that is likely to be able to target  IncFIIK/IncFIB(K)  plasmids presumably facilitating intracellular, inter-plasmid competition.

Identification of a Type IV-A CRISPR-Cas System Located Exclusively on IncHI1B/IncFIB Plasmids in Enterobacteriaceae