Abstract
Background: Molecular typing is essential for inferring genetic relatedness between bacterial pathogens. In this study, we applied whole genome sequencing (WGS) for rapid prediction of sequence type and antibiotic resistance for invasive pneumococcal isolates.Methods: 240 isolates from adults (≥50 years old) in Ontario, Canada during 2009 to 2013 were subjected to WGS. Sequence type, antibiotic susceptibility and resistance were predicted directly from short reads. Emerging non-vaccine serotype 22F was further characterized by WGS.Results: Sequence type was successfully determined for 98.3% of isolates. The overall sensitivity and specificity for antibiotic resistance prediction were 95 and 100% respectively, compared to standard susceptibility testing methods. WGS-based phylogeny divided emerging 22F (ST433) strains into two distinct clades: clade A harboring a 23 kb-prophage and anti-phage PhD/Doc system and clade B with virulence-related proteases. Five isolates in clade A developed macrolide resistance via 5.1 kb mega element recombination (encoding mefE and msrD), while one isolate in clade B displayed quinolone resistance via a gyrA mutation.Conclusions: WGS is valuable for routine surveillance of pneumococcal clinical isolates and facilitates prediction of genotype and antibiotic resistance. The emergence of 22F in Ontario in the post-vaccine era and evidence of evolution and divergence of the 22F population warrants heightened pneumococcal molecular surveillance.
Highlights
Invasive pneumococcal diseases (IPD) such as septicaemia and meningitis caused by Streptococcus pneumoniae result in a heavy burden of disease among children and adults worldwide (Ausina et al, 1988; O’Brien et al, 2007)
IPD isolates were voluntarily submitted to Public Health Ontario Laboratories (PHOL) from regional health units, distribution map of clinical samples indicated a good representation of geographic regions in the province of Ontario (Figure S1)
Overall, during 2009–2013 IPD cases in older adults (≥50 years of age) due to PCV13 serotypes showed the trend of decline, while IPDs due to non-PCV13 serotypes had the trend of increase (Figure 1)
Summary
Invasive pneumococcal diseases (IPD) such as septicaemia and meningitis caused by Streptococcus pneumoniae result in a heavy burden of disease among children and adults worldwide (Ausina et al, 1988; O’Brien et al, 2007). After widespread implementation in 2002 of the 7-valent pneumococcal conjugate vaccine (PCV7, covering serotypes 4, 6B, 9V, 14, 18C, 19F, and 23F) in Canadian children, the incidence of IPD due to PCV7 serotypes decreased significantly in all age groups within the Canadian population (Kellner et al, 2009). In addition to use in children, the PCV13 vaccine was approved by Canadian health authorities in 2012 for use among adults 50 years and older for the prevention of IPD (An Advisory Committee Statement (ACS), 2013). It is recommended for immunocompromised adults aged ≥ 18 years with high risk of IPD (An Advisory Committee Statement (ACS), 2013; Tomczyk et al, 2014). We applied whole genome sequencing (WGS) for rapid prediction of sequence type and antibiotic resistance for invasive pneumococcal isolates
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