The purpose of this study is to systematically identify

the primers unable to obtain the correct sequence, describe an alternative set of primers, and introduce documentation to the literature offering additional Fludarabine order guidance to groups undertaking S. pneumoniae MLST studies. In this investigation, the effectiveness of the standard MLST sequencing primers, and an alternate set of primers were evaluated for their ability to completely sequence, in both directions, the appropriate typing regions of each gene. Results This analysis consistently observed that the forward and reverse sequences obtained with the standard MLST primers only completely covered the typing

region for two of the seven genes: gki Selumetinib mouse and gdh. The reverse primer for the aroE, and recP genes failed to sequence the last 21 and 10 bases of their respective typing regions (Figure 1A, and B). The forward spi and xpt MLST primers do not sequence the first 6 and 17 bases of their respective typing regions (Figure 1C and D). In the case of ddl, the forward primer was unable to sequence the first 8 bases (Figure 1E) and the reverse did not sequence the last 26 bases (Figure 1F). These observations were consistent across all of the different isolates, both sequencing services, and each replicate. In each of the cases that the full sequence was not obtained, the alignment of the primers with publically available genomic sequences for S. pneumoniae identified Sodium butyrate that those primers annealed less than 30 base pairs from the required typing region (Figure 1). Figure 1 S. pneumoniae MLST typing regions for each of the segments not fully sequenced by the standard primers aligned with a section of the corresponding genomic DNA. Panels (A) through (F) identify each individual gene and direction combination, for which the complete typing region is not obtained. The black arrows depict the binding sites of the standard primers to the up or downstream genomic DNA. The line marked boxes

identify the segment that is consistently not obtained by sequencing with the standard primers. The angle bracket and top sequence identify either the 5’ or 3’ end of the typing region depending on the specific MLST gene. A partial set of modified MLST primers for S. pneumoniae were designed and introduced by the US Centers for Disease Control (CDC) [12]. The CDC primers for aroE, the reverse primer for recP, and the forward primer of ddl each annealed within the coding sequence for the gene possessing the typing region, and were able to completely cover the required sequence. However, the CDC forward primer for recP, and both sets of spi and xpt primers annealed to regions of genomic DNA outside of their target gene.