The lactococcal plasmid-derived defences against phages

Lactococcus lactis and Lactococcus cremoris represent bacteria of economic and industrial importance due to their extensive application in the production of fermented foods. Their intensive application is associated with the emergence of bacteriophages which are ubiquitous in the (non-sterile) dairy environment. Phage infection may cause lysis of the starter culture, resulting in delayed or even failed fermentations with negative economic consequences. To defend themselves against phages, bacteria have adopted multiple resistance strategies. Abortive infection (Abi) systems represent one of the most common lactococcal anti-phage mechanisms and are usually plasmid-encoded. They are activated at a step after phage DNA injection leading to cell death and therefore to the protection of the rest of the bacterial community from infection. In this study, the genomes of 53 lactococcal strains in our collection were sequenced by using a combination of Pacific Biosciences RS II and Illumina sequencing approaches. As Lactococcus is reported to harbour up to 12 plasmids and these mobile elements are presumed to confer some benefit on the host including phage resistance, the plasmidomes were extracted and annotated by using tools such as Pfam and HHpred. 321 plasmid sequences were analysed for the presence of novel anti-phage systems and the 23 established lactococcal Abi systems. This resulted in the detection of approximately 50% of the known Abi systems (eight Abi, 100% aa identity & two Abi-like systems) and several novel systems. These systems were cloned, and their anti-phage effect was assessed against a panel of phages representing four lactococcal phage groups.