FIG 7.

Genomic organization and PCR validation of SpST71A. (A) Chromosomal region of an ST71 genome (NCBI accession CP016073) with integrated SpST71A prophage shown in red. SpST71A is integrated in the middle of comGA (dark green arrow) splitting the gene into two parts, indicated by asterisks (*). The other ORFs of the comG operon (comGB, comGC, comGD, comGE, comGF, and comGG) are also indicated. An intact comG operon, without SpST71A prophage, in a non-ST71 genome (NCBI accession CP015626) is also shown for comparison. The ComGAF1, ComGAR1, and IntegR1 primers used for PCR screening of SpST71A are shown as small black arrows. The prophage ORFs whose functional annotations could not be predicted by eggNOG are identified by their locus tag. The functional annotation of all prophage ORFs is provided in Table S4 in the supplemental material. The linear comparison figure was created using Easyfig. (B) Schematic representation of the SpST71A insertion site and PCR amplification strategy. (C) A representative DNA agarose gel showing PCR screening of SpST71A prophage using ComGAF1/ComGAR1 and ComGAF1/IntegR1 primer pairs. Both set of PCRs were performed on all 50 isolates sequenced in this study. As shown, ComGAF1/ComGAR1 PCR could not amplify the 45,110-bp region (SpST71A) expected in ST71 but amplified the 518-bp comGA fragment in all non-ST71 isolates. ComGAF1/IntegR1 PCR amplified the 945-bp region in all ST71 isolates but not in other isolates. PTTMP, phage tail tape measure protein.