Refined analyses suggest that recombination is a minor source of genomic diversity in Pseudomonas aeruginosa chronic cystic fibrosis infections

Chronic bacterial airway infections in people with cystic fibrosis (CF) are often caused by Pseudomonas aeruginosa, typically showing high phenotypic diversity amongst co-isolates from the same sputum sample. Whilst adaptive evolution during chronic infections has been reported, the genetic mechanisms underlying the observed rapid within-population diversification are not well understood. Two recent conflicting reports described very high and low rates of homologous recombination in two closely related P. aeruginosa populations from the lungs of different chronically infected CF patients. To investigate the underlying cause of these contrasting observations, we combined the short read datasets from both studies and applied a new comparative analysis. We inferred low rates of recombination in both populations. The discrepancy in the findings of the two previous studies can be explained by differences in the application of variant calling techniques. Two novel algorithms were developed that filter false-positive variants. The first algorithm filters variants on the basis of ambiguity within duplications in the reference genome. The second omits probable false-positive variants at regions of non-homology between reference and sample caused by structural rearrangements. As gains and losses of prophage or genomic islands are frequent causes of chromosomal rearrangements within microbial populations, this filter has broad appeal for mitigating false-positive variant calls. Both algorithms are available in a Python package.