Pradeep Reddy Marri led a comparative whole-genome sequencing study of commensal and pathogenic Neisseria. The 2010 paper found that commensal species carry many virulence alleles and have extensive genetic exchange with other Neisseria. A harmless colonizer can therefore be a reservoir of genetic variants relevant to a pathogenic relative.[ref]
This connects horizontal gene transfer to the evolution of disease-associated traits. Possessing a particular allele does not by itself establish pathogenicity: its genomic context, regulation and host interaction also matter.

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