Whole-Genome Sequencing Reveals the Origin and Rapid Evolution of an Emerging Outbreak Strain ofStreptococcus pneumoniae12F

Abstract

Background. Streptococcus pneumoniae is a major cause of community-acquired pneumonia and septicemia in adults. The global drug-susceptible capsular serotype 12F, clonal complex 218 caused several outbreaks in the United States between 1989 and 2008, as well as a recent large outbreak in Manitoba, Canada, that resulted in 36 cases of septicemia and 3 deaths. The evolutionary origin of the Canadian outbreak strain and its relationship to the historical US outbreak strains are not known.Methods. Whole-genome deep sequencing was performed on isolates from the Canadian outbreak (n = 36), the US outbreaks (n = 9), and nonoutbreak surveys (n = 21). Phylogenomic analysis and comparative genomics were used to assess evolutionary relationships and to detect gene content differences between the isolates.Results. The Canadian outbreak was closely related to sporadic cases that occurred preoutbreak in cross-border geographic regions in Manitoba, North Dakota, and Iowa. The emerging Canadian strain differed from US strains by acquisition of a cell-surface protein and macrolide resistance determinants via incorporation of a 5.3-kb mega cassette harboring msrD and mefE. Furthermore, during 11 months of transmission, this clone evolved rapidly and acquired fluoroquinolone resistance through precise stepwise mutations in both parC and gyrA, and putative compensatory mutations in uraA or IMPDH under drug selection. Alarmingly, this drug-resistant clone appears to have spread quickly to other regions of Canada and the United States, and replaced drug-susceptible strains.Conclusions. Whole-genome sequencing revealed an independent emergence and secondary adaptation of a new virulent and drug-resistant pneumococcal epidemic clone. Ongoing molecular surveillance is required, and measures to prevent its spread should be developed.

Epidemiology of invasive pneumococcal and Haemophilus influenzae diseases in Northwestern Ontario, Canada, 2010–2015

“…One of the most prevalent S. pneumoniae serotypes, 12F (14%), has undergone whole-genome sequencing, revealing secondary adaptation to a new virulent and drugresistant form (Deng et al, 2016). This form was first identified in an epidemic in Manitoba, Canada (geographically very close to Northwestern Ontario), and has since spread to multiple sites across Canada and the USA (Deng et al, 2016). In the paediatric population of this study, all IPD cases were caused by non-PCV serotypes.…”

“…Although the PPV-23 vaccine protects against the most virulent and prevalent pneumococcal serotypes (1, 2, 3, 4, 5, 6B, 7F, 8, 9N, 9V, 10A, 11A, 12F, 14, 15B, 17F, 18C, 19A, 19F, 20, 22F, 23F, and 33F) and is effective in preventing adult IPD, it is less effective against non-invasive infections and is ineffective in young children (Kellner and Tyrrell, 2005).Of note, the PPV-23 vaccine contains the serotypes of 70.3% of all identified S. pneumoniae serotypes for SLMHC cases (67.7% of cases in people >5 years; 62.5% of cases in people >65 years). One of the most prevalent S. pneumoniae serotypes, 12F (14%), has undergone whole-genome sequencing, revealing secondary adaptation to a new virulent and drugresistant form (Deng et al, 2016). This form was first identified in an epidemic in Manitoba, Canada (geographically very close to Northwestern Ontario), and has since spread to multiple sites across Canada and the USA (Deng et al, 2016).…”

Pneumococcal lineages associated with serotype replacement and antibiotic resistance in childhood invasive pneumococcal disease in the post-PCV13 era: an international whole-genome sequencing study

“…Increases in serotype 12F resulting in disease replacement were reported in England and Wales, 6 France, 9,40 and Germany, 39 although the genotypes of those isolates were not reported. Globally, serotype 12F isolates mainly belong to clonal complex (CC) 989 (GPSC26), 41,42 but also to ST218 (GPSC32) in North America 43,44 and CC3524 (GPSC55), a regional lineage, in Israel. Increase in serotype 8 was also observed among children less than 5 years of age in England and Wales in 2016-17.…”

Long-term trends in invasive pneumococcal disease in Manitoba, Canada

“…16 However, the Winnipeg outbreak was caused by a rapidly evolving novel 12F clone, ST218, that acquired both macrolide and fluoroquinolone resistance via recombination with a 5.3 kb mega gene cassette harboring msrD and mefE as well as several mutations. 17 The Manitoba clone appears to have spread to neighboring Canadian and US jurisdictions replacing drug-sensitive strains. 17 Our study confirmed that the burden of IPD in Manitoba remained high among groups previously identified at higher risk including the poor and those with chronic diseases.…”

“…17 The Manitoba clone appears to have spread to neighboring Canadian and US jurisdictions replacing drug-sensitive strains. 17 Our study confirmed that the burden of IPD in Manitoba remained high among groups previously identified at higher risk including the poor and those with chronic diseases. Manitoba's overall rates were in line with Canadian rates, whereas the rates reported in northern Manitoba and inner city Winnipeg, both communities that are socio-economically disadvantaged and pre-dominantly of indigenous ethnicity, were significantly higher.…”