Comparative genomic analysis of a wild-type strain of the ovine pathogen Chlamydia abortus and its nitrosoguanidine-induced, temperature-sensitive, virulence-attenuated live vaccine derivative identified 22 single nucleotide polymorphisms unique to the mutant, including nine nonsynonymous mutations, one leading to a truncation of pmpG, which encodes a polymorphic membrane protein, and two intergenic mutations potentially affecting promoter sequences. Other nonsynonymous mutations mapped to a pmpG pseudogene and to predicted coding sequences encoding a putative lipoprotein, a sigma-54-dependent response regulator, a PhoH-like protein, a putative export protein, two tRNA synthetases, and a putative serine hydroxymethyltransferase. One of the intergenic mutations putatively affects transcription of two divergent genes encoding pyruvate kinase and a putative SOS response nuclease, respectively. These observations suggest that the temperature-sensitive phenotype and associated virulence attenuation of the vaccine strain result from disrupted metabolic activity due to altered pyruvate kinase expression and/or alteration in the function of one or more membrane proteins, most notably PmpG and a putative lipoprotein.The Chlamydiaceae represent a group of obligate intracellular bacteria responsible for a wide range of diseases in many different hosts with significant and broad economic and public health impacts. Despite the global impact of chlamydial disease, vaccines are available for only two chlamydial species, Chlamydia abortus and Chlamydia felis, which infect ovine and feline species, respectively. A formalin-inactivated vaccine against C. abortus infection, which in the United Kingdom costs the agricultural industry an estimated £20 million each year (2), was developed in the 1960s but did not offer complete protection and required revaccination every 3 years. This vaccine subsequently became demonstrably ineffective when C. abortus infections occurred in vaccinated flocks in the late 1970s (1, 14). Although inactivated vaccines are still used, more effective C. felis and C. abortus vaccines derived from live attenuated strains are also available. However, C. felis reinfection is not completely controlled with the live attenuated C. felis vaccine, as vaccinated animals still shed chlamydiae (32). In contrast, the live attenuated C. abortus vaccine blocks reinfection and shedding (24, 25).The C. abortus vaccine is based on a live attenuated strain obtained by nitrosoguanidine (NTG) mutagenesis of the virulent strain AB7, isolated from an aborted lamb (8). NTG causes mutations by methylation of nucleotides, especially of guanine, which can then pair with thymine or cytosine (16), giving rise to a GC-to-AT conversion. Other nucleotide substitutions are seen less frequently with deletions resulting from lesion repair. Treatment of AB7 with NTG produced two temperature-sensitive mutants, 1B and 1H, which were attenuated in the mouse model (21). Unlike 1H, which was unstable in temperature-sensitive growth studies, the ...