Occurrence of type VI secretion system effector genes in longitudinal isolates of P. aeruginosa from people with cystic fibrosis

<i>Pseudomonas aeruginosa</i> uses multiple type VI secretion systems (T6SSs) to manipulate eukaryotic cells, kill competing microbes and take up nutrients. Bacterial strains are known to differ in their T6SS apparatus and the toxic effector proteins responsible for killing. The ability to eliminate competitors has been repeatedly demonstrated in lab studies, but much less is known about effector genotypes during infection. We used comparative genomics to test for the presence and absence of T6SS effector genes in over 450 clinical <i>P. aeruginosa</i> isolates from people with cystic fibrosis in Copenhagen (Denmark) and complemented these findings with data of 52 isolates from people with cystic fibrosis in London (UK). We found natural variation in the occurrence and combination of effector genes. Patients were typically infected with isolates that differ in their effector gene sets but show no statistically significant association between the number of effector genes and chronic infection. Isolates with a pair of T6SS effector and immunity genes and isolates without these genes, which would be expected to kill each other based on existing work in the laboratory, were found on the same individual. Taking the isolates' phylogeny and sampling times into account, we identified five putative loss events of effector genes during infection. Although the impact of our findings for infected individuals will require further investigation, we demonstrate the extent of strain-level variation in T6SS effector genes in clinical isolates.