Genetic Diversity of the Q Fever Agent,Coxiella burnetii, Assessed by Microarray-Based Whole-Genome Comparisons

Abstract

Coxiella burnetii, a gram-negative obligate intracellular bacterium, causes human Q fever and is considered a potential agent of bioterrorism. Distinct genomic groups of C. burnetii are revealed by restriction fragmentlength polymorphisms (RFLP). Here we comprehensively define the genetic diversity of C. burnetii by hybridizing the genomes of 20 RFLP-grouped and four ungrouped isolates from disparate sources to a high-density custom Affymetrix GeneChip containing all open reading frames (ORFs) of the Nine Mile phase I (NMI) reference isolate. We confirmed the relatedness of RFLP-grouped isolates and showed that two ungrouped isolates represent distinct genomic groups. Isolates contained up to 20 genomic polymorphisms consisting of 1 to 18 ORFs each. These were mostly complete ORF deletions, although partial deletions, point mutations, and insertions were also identified. A total of 139 chromosomal and plasmid ORFs were polymorphic among all C. burnetii isolates, representing ca. 7% of the NMI coding capacity. Approximately 67% of all deleted ORFs were hypothetical, while 9% were annotated in NMI as nonfunctional (e.g., frameshifted). The remaining deleted ORFs were associated with diverse cellular functions. The only deletions associated with isogenic NMI variants of attenuated virulence were previously described large deletions containing genes involved in lipopolysaccharide (LPS) biosynthesis, suggesting that these polymorphisms alone are responsible for the lower virulence of these variants. Interestingly, a variant of the Australia QD isolate producing truncated LPS had no detectable deletions, indicating LPS truncation can occur via small genetic changes. Our results provide new insight into the genetic diversity and virulence potential of Coxiella species.

Coxiella burnetiiIsolates Cause Genogroup-Specific Virulence in Mouse and Guinea Pig Models of Acute Q Fever

“…The infection studies described here illustrate that there is pathotype diversity between C. burnetii isolates from different genogroups, and they are consistent with phylogenetic studies cataloging distinct gene contents (4). We therefore strove to determine whether this diversity was great enough to affect the ability of vaccines to protect against infection.…”

“…These monophyletic groups supported the early RFLP groups and placed groups I, II, and III in one monophyletic group; group IV in the second monophyletic group; and group V in the third monophyletic group. A comprehensive microarray-based whole-genome comparison by Beare et al confirmed the relatedness of RFLP-grouped isolates and added two more genomic groups, VII and VIII (4). Differences in novel gene contents and pseudogenes may be factors in the variations in virulence seen among group I, IV, V, and VI isolates (5).…”

Right on Q: Genetics begin to Unravel Coxiella Burnetii host cell Interactions

“…O-antigen is the primary surface antigen recognized by Phase I antiserum [25]. Some, but not all, Phase II strains contain a chromosomal deletion eliminating roughly 20 genes associated with sugar metabolism [26][27][28]. Moreover, deep-rough LPS of Phase II strains can be antigenically distinct [29].…”

Host cell-free growth of the Q fever bacterium Coxiella burnetii

“…All cRNA originating from Vero cell-propagated C. burnetii and 3 g cRNA from CCM-cultivated organisms were hybridized to a custom Affymetrix GeneChip designed as previously described (35). Microarray data were analyzed using Partek Genomics Suite software (Partek Inc.) essentially as described (36).…”