Deng Xianding, Memari Nader, Teatero Sarah, Athey Taryn, Isabel Marc, Mazzulli Tony, Fittipaldi Nahuel, Gubbay Jonathan B
Public Health Ontario LaboratoryToronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of TorontoToronto, ON, Canada; Mount Sinai Hospital and University Health NetworkToronto, ON, Canada.
Public Health Ontario Laboratory Toronto, ON, Canada.
Front Microbiol. 2016 Dec 27;7:2099. doi: 10.3389/fmicb.2016.02099. eCollection 2016.
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. 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. 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 and ), while one isolate in clade B displayed quinolone resistance via a mutation. 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.
分子分型对于推断细菌病原体之间的遗传相关性至关重要。在本研究中，我们应用全基因组测序（WGS）对侵袭性肺炎球菌分离株的序列类型和抗生素耐药性进行快速预测。对2009年至2013年期间从加拿大安大略省的成年人（≥50岁）中分离出的240株菌株进行了WGS分析。直接从短读长序列预测序列类型、抗生素敏感性和耐药性。通过WGS对新出现的非疫苗血清型22F进行了进一步表征。98.3%的分离株成功确定了序列类型。与标准药敏试验方法相比，抗生素耐药性预测的总体敏感性和特异性分别为95%和100%。基于WGS的系统发育分析将新出现的22F（ST433）菌株分为两个不同的进化枝：进化枝A含有一个23 kb的前噬菌体和抗噬菌体PhD/Doc系统，进化枝B含有与毒力相关的蛋白酶。进化枝A中的5株分离株通过5.1 kb的大元件重组（编码 和 ）产生了大环内酯耐药性，而进化枝B中的1株分离株通过 突变表现出喹诺酮耐药性。WGS对于肺炎球菌临床分离株的常规监测很有价值，有助于预测基因型和抗生素耐药性。疫苗接种后时代安大略省22F血清型的出现以及22F群体进化和分化的证据表明有必要加强肺炎球菌分子监测。
