{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,28]],"date-time":"2026-05-28T01:15:13Z","timestamp":1779930913637,"version":"3.53.1"},"reference-count":35,"publisher":"Microbiology Society","issue":"7","license":[{"start":{"date-parts":[[2018,7,1]],"date-time":"2018-07-01T00:00:00Z","timestamp":1530403200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,7,1]]},"abstract":"<jats:p>Distinuishing the species of mitis group streptococci is challenging due to ambiguous phenotypic characteristics and high degree of genetic similarity. This has been particularly true for resolving atypical <jats:italic>Streptococcus pneumoniae<\/jats:italic> and <jats:italic>Streptococcus pseudopneumoniae<\/jats:italic>. We used phylogenetic clustering to demonstrate specific and separate clades for both <jats:italic>S. pneumoniae<\/jats:italic> and <jats:italic>S. pseudopneumoniae<\/jats:italic> genomes. The genomes that clustered within these defined clades were used to extract species-specific genes from the pan-genome. The <jats:italic>S. pneumoniae<\/jats:italic> marker was detected in 8027 out of 8051 (&gt;99.7\u200a%) <jats:italic>S. pneumoniae<\/jats:italic> genomes. The <jats:italic>S. pseudopneumoniae<\/jats:italic> marker was specific for all genomes that clustered in the <jats:italic>S. pseudopneumoniae<\/jats:italic> clade, including unresolved species of the genus <jats:italic>Streptococcus<\/jats:italic> sequenced by the BC Centre for Disease Control Public Health Laboratory that previously could not be distinguished by other methods. Other than the presence of the <jats:italic>S. pseudopneumoniae<\/jats:italic> marker in six of 8051 (&lt;0.08\u200a%) <jats:italic>S. pneumoniae<\/jats:italic> genomes, both the <jats:italic>S. pneumoniae<\/jats:italic> and <jats:italic>S. pseudopneumoniae<\/jats:italic> markers showed little to no detectable cross-reactivity to the genomes of any other species of the genus <jats:italic>Streptococcus<\/jats:italic> or to a panel of over 46\u200a000\u2009genomes from viral, fungal, bacterial pathogens and microbiota commonly found in the respiratory tract. A real-time PCR assay was designed targeting these two markers. Genomics provides a useful technique for PCR assay design and development.<\/jats:p>","DOI":"10.1099\/mgen.0.000175","type":"journal-article","created":{"date-parts":[[2018,4,9]],"date-time":"2018-04-09T14:12:43Z","timestamp":1523283163000},"source":"Crossref","is-referenced-by-count":14,"title":["Use of genomics to design a diagnostic assay to discriminate between Streptococcus pneumoniae and Streptococcus pseudopneumoniae"],"prefix":"10.1099","volume":"4","author":[{"given":"Matthew A.","family":"Croxen","sequence":"first","affiliation":[{"name":"2\u200bProvincial Laboratory for Public Health (ProvLab), University of Alberta Hospital, Edmonton, Alberta, Canada"},{"name":"\u2021\u200bPresent address: Provincial Laboratory for Public Health, Edmonton, Canada."},{"name":"\u00a7\u200bPresent address: Department of Laboratory Medicine & Pathology, University of Alberta, Edmonton, Canada."},{"name":"1\u200bBC Centre for Disease Control Public Health Laboratory, Vancouver, 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