Intrastrain and interstrain genetic variation within a paralogous gene family in Chlamydia pneumoniae

Comparative analysis of this gene family within the published genome sequences provided evidence that multiple levels of genetic variation are evident within this single collection of paralogous genes. Frameshift mutations are found that result in both truncated gene products and pseudogenes that vary among isolates. Several genes in this family contain polycytosine (polyC) tracts either upstream or within the terminal 5' end of the predicted coding sequence. The length of the polyC stretch varies between paralogous genes and within single genes in the three genomes. Sequence analysis of genomic DNA from a collection of 12 C. pneumoniae clinical isolates was used to determine the extent of the variation in the Cpn 1054 gene family.These studies demonstrate that sequence variability is present both among strains and within strains at several of the loci. In particular, changes in the length of the polyC tract associated with the different Cpn 1054 gene family members are common within each tested C. pneumoniae isolate. The variability identified within this newly described gene family may modulate either phase or antigenic variation and subsequent physiologic diversity within a C. pneumoniae population.Chlamydia pneumoniae is an obligate intracellular bacterium that infects and causes disease in the respiratory tract [1,2] and has recently been associated with heart disease [3]. Approximately 10% of pneumoniae cases and 5% of bronchitis and sinusitis cases in the U.S. are attributed to C. pneumoniae infection. Pathogenic mechanisms utilized by C. pneumoniae to replicate and disseminate within hosts remain unclear.Little is known about strain-specific determinants of C. pneumoniae. Isolates of C. pneumoniae are virtually indistinguishable using 16s rRNA [4], restriction fragment length polymorphism [5], and amplification fragment length polymorphism analysis [6]. Unlike C. trachomatis, only a single serotype or genotype of C. pneumoniae has been identified by any of t