FIG. 4.

Repeat region B mgpB sequences identified in cervical specimens from participant no. 10139, a woman persistently infected with M. genitalium. A total of 40 sequences (10 per cervical sample) were analyzed, and 17 unique variants (A to Q) were detected in the four time points examined. (A) Schematic representation of the 17 sequences identified. White regions are homologous to the published G-37^T sequence, while areas shaded as indicated by the key diverge from the mgpB sequence and instead have homology to G-37^T MgPar sequences or have no homology to any sequences in the G-37^T genome (designated “novel”). Block sizes shown in the key represent five nucleotides each. Sequence I contained an extra adenosine base (shown with an A) at bp 878, which is predicted to alter the reading frame and introduce three in-frame stop codons, indicated with red arrows. The schematically depicted sequences are presented in more detail in panels B and C. (B) Sequence alignment of mgpB bp 620 to 709 of G-37^T; patient no. 10139 sequences A, B, D, E, and I; and the G-37^T MgPar sequences showing the chimeric nature of mgpB sequences and possible explanations for their generation. Sequence A or B could have initially recombined with MgPar 4 to generate sequence D, which then could have recombined with novel sequence 1 to generate sequence E or I. (C) The shift in mgpB sequences over the course of a persistent infection exemplified by an alignment between sequences A through Q and the published G-37^T mgpB sequence between bp 767 to 816. Bases with identity to the G-37^T mgpB sequence are highlighted in gray, while bases identified as novel sequences 3 and 4 are shaded in red and yellow, respectively. The horizontal arrows at the top and bottom of panels A and C, respectively, indicate the conserved sequence targeted by primer 2R (Fig. 2; Table 2) used in the strain typing experiments. Sequences A through Q have been deposited in GenBank under accession numbers DQ248070 through DQ248086, respectively.