Whole Genome Analysis of Streptococcus pneumoniae Serotype 4 Causing Outbreak of Invasive Pneumococcal Disease, Alberta, Canada

After the introduction of pneumococcal conjugate vaccines for children, invasive pneumococcal disease caused by Streptococcus pneumoniae serotype 4 declined in all ages in Alberta, Canada, but it has reemerged and spread in adults in Calgary, primarily among persons who are experiencing homelessness or who use illicit drugs. We conducted clinical and molecular analyses to examine the cases and isolates. Whole-genome sequencing analysis indicated relatively high genetic variability of serotype 4 isolates. Phylogenetic analysis identified 1 emergent sequence type (ST) 244 lineage primarily associated within Alberta and nationally distributed clades ST205 and ST695. Isolates from 6 subclades of the ST244 lineage clustered regionally, temporally, and by homeless status. In multivariable logistic regression, factors associated with serotype 4 invasive pneumococcal disease were being male, being <65 years of age, experiencing homelessness, having a diagnosis of pneumonia or empyema, or using illicit drugs.

Automated summary

After the introduction of pneumococcal conjugate vaccines in children, invasive pneumococcal disease caused by Streptococcus pneumoniae serotype 4 decreased in all ages in Alberta, Canada, but has reemerged and spread among adults in Calgary, particularly among individuals experiencing homelessness or using illicit drugs. Molecular analysis indicated high genetic variability of serotype 4 isolates. Phylogenetic analysis identified an emergent sequence type 244 lineage primarily associated within Alberta and nationally distributed clades ST205 and ST695.