Large scale genomic analysis shows no evidence for repeated pathogen adaptation during the invasive phase of bacterial meningitis in humans

Recent studies have provided evidence for rapid pathogen genome variation, some of which could potentially affect the course of disease. We have previously detected such variation by comparing isolates infecting the blood and cerebrospinal fluid (CSF) of a single patient during a case of bacterial meningitis.\n\nTo determine whether the observed variation repeatedly occurs in cases of disease, we performed whole genome sequencing of paired isolates from blood and CSF of 938 meningitis patients. We also applied the same techniques to 54 paired isolates from the nasopharynx and CSF.\n\nUsing a combination of reference-free variant calling approaches we show that no genetic adaptation occurs in the invasive phase of bacterial meningitis for four major pathogen species: Streptococcus pneumoniae, Neisseria meningitidis, Listeria monocytogenes and Haemophilus influenzae. From nasopharynx to CSF, no adaptation was seen in S. pneumoniae, but in N. meningitidis mutations potentially mediating adaptation to the invasive niche were occasionally observed in the dca gene.\n\nThis study therefore shows that the bacteria capable of causing meningitis are already able to do this upon entering the blood, and no further sequence change is necessary to cross the blood-brain barrier. The variation discovered from nasopharyngeal isolates suggest that larger studies comparing carriage and invasion may help determine the likely mechanisms of invasiveness.\n\nAuthor SummaryWe have analysed the entire DNA sequence from bacterial pathogen isolates from cases of meningitis in 938 Dutch adults, focusing on comparing pairs of isolates from the patients blood and their cerebrospinal fluid. Previous research has been on only a single patient, but showed possible signs of adaptation to treatment within the host over the course of a single case of disease.\n\nBy sequencing many more such paired samples, and including four different bacterial species, we were able to determine that adaptation of the pathogen does not occur after bloodstream invasion during bacterial meningitis.\n\nWe also analysed 54 pairs of isolates from pre- and post-invasive niches from the same patient. In N. meningitidis we found variation in the sequence of one gene which appears to provide bacteria with an advantage after invasion of the bloodstream.\n\nOverall, our findings indicate that evolution after invasion in bacterial meningitis is not a major contribution to disease pathogenesis. Future studies should involve more extensive sampling between the carriage and disease niches, or on variation of the host.