1887

Abstract

. Correct serotype identification of (pneumococcus) is important for monitoring disease epidemiology and assessing the impacts of pneumococcal vaccines. Furthermore, correct identification and differentiation of the pathogenic from closely related commensal species of the mitis group of the genus are essential for correct serotype identification.

. A new protocol for determining the existing 98 serotypes of pneumococcus was developed, applying two PCR amplifications and amplicon sequencing, using newly designed internal primers. The new protocol was validated using genome sequences, reference strains with confirmed serotypes and clinical isolates, and comparing the results with those from the traditional Quellung reaction or antiserum panel gel precipitation, in addition to real-time PCR analysis. The taxonomic identifications of 422 publicly available (GenBank) genome sequences of and were assessed by whole-genome sequence average nucleotide identity based on (ANIb) analysis.

. The proposed sequetyping protocol generates a 1017 bp whole region sequence, increasing resolution for serotype identification in pneumococcus isolates. The identifications of all GenBank genome sequences of were confirmed, whereas most of the and almost all of the genome sequences did not fulfil the ANIb thresholds for species-level identification. The housekeeping biomarker gene, , correctly identified but often misclassified and as .

. These studies affirm the importance of applying reliable identification protocols for before serotyping; our protocols provide reliable diagnostic tools, as well as an improved workflow, for serotype identification of pneumococcus and differentiation of serogroup 6 types.

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/content/journal/jmm/10.1099/jmm.0.001022
2019-08-01
2019-10-22
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