Rapid Typing of Coxiella burnetii

Abstract

Coxiella burnetii has the potential to cause serious disease and is highly prevalent in the environment. Despite this, epidemiological data are sparse and isolate collections are typically small, rare, and difficult to share among laboratories as this pathogen is governed by select agent rules and fastidious to culture. With the advent of whole genome sequencing, some of this knowledge gap has been overcome by the development of genotyping schemes, however many of these methods are cumbersome and not readily transferable between institutions. As comparisons of the few existing collections can dramatically increase our knowledge of the evolution and phylogeography of the species, we aimed to facilitate such comparisons by extracting SNP signatures from past genotyping efforts and then incorporated these signatures into assays that quickly and easily define genotypes and phylogenetic groups. We found 91 polymorphisms (SNPs and indels) among multispacer sequence typing (MST) loci and designed 14 SNP-based assays that could be used to type samples based on previously established phylogenetic groups. These assays are rapid, inexpensive, real-time PCR assays whose results are unambiguous. Data from these assays allowed us to assign 43 previously untyped isolates to established genotypes and genomic groups. Furthermore, genotyping results based on assays from the signatures provided here are easily transferred between institutions, readily interpreted phylogenetically and simple to adapt to new genotyping technologies.

Presence and Persistence of Coxiella burnetii in the Environments of Goat Farms Associated with a Q Fever Outbreak

“…DNA was purified from the isolates using the QIAamp DNA minikit tissue protocol (Qiagen). Base pair assignments at 14 single nucleotide polymorphisms (SNPs) were made using SNP genotyping assays as described previously (17).…”

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

“…SNP-based typing has revealed 35 unique genotypes of Coxiella [11,17,18]. Some genotypes have defined associations with animal reservoirs and disease in humans.…”

“…Some genotypes have defined associations with animal reservoirs and disease in humans. For example, genotype 8 has a goat reservoir and is associated with human chronic disease [18]. Researchers hypothesize that this genotype is more likely to cause a subclinical infection that goes untreated, thereby persisting and causing chronic disease such as endocarditis [18].…”

“…For example, genotype 8 has a goat reservoir and is associated with human chronic disease [18]. Researchers hypothesize that this genotype is more likely to cause a subclinical infection that goes untreated, thereby persisting and causing chronic disease such as endocarditis [18]. Genotype 17 is associated with severe, acute Q fever pneumonia in French Guiana [19].…”

“…The vast majority (>96%) of Dot/Icm substrates have been identified using the genome of the NMI RSA493 strain (multispacer sequencing typing genotype 18, 26), which is highly virulent [16,18] 18,118], showed that many effector genes are pseudogeneized, due to insertion/deletions resulting in frameshifts, or completely missing (Figure 1). Indeed, only 44 out of 143 identified effector genes are intact among all 5 strains.…”