Rapid typing of Coxiella burnetii

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

High prevalence and two dominant host-specific genotypes of Coxiella burnetii in U.S. milk

BackgroundCoxiella burnetii causes Q fever in humans and Coxiellosis in animals; symptoms range from general malaise to fever, pneumonia, endocarditis and death. Livestock are a significant source of human infection as they shed C. burnetii cells in birth tissues, milk, urine and feces. Although prevalence of C. burnetii is high, few Q fever cases are reported in the U.S. and we have a limited understanding of their connectedness due to difficulties in genotyping. Here, we develop canonical SNP genotyping assays to evaluate spatial and temporal relationships among C. burnetii environmental samples and compare them across studies. Given the genotypic diversity of historical collections, we hypothesized that the current enzootic of Coxiellosis is caused by multiple circulating genotypes. We collected A) 23 milk samples from a single bovine herd, B) 134 commercial bovine and caprine milk samples from across the U.S., and C) 400 bovine and caprine samples from six milk processing plants over three years.ResultsWe detected C. burnetii DNA in 96% of samples with no variance over time. We genotyped 88.5% of positive samples; bovine milk contained only a single genotype (ST20) and caprine milk was dominated by a second type (mostly ST8).ConclusionsThe high prevalence and lack of genotypic diversity is consistent with a model of rapid spread and persistence. The segregation of genotypes between host species is indicative of species-specific adaptations or dissemination barriers and may offer insights into the relative lack of human cases and characterizing genotypes

Transmission efficiency of the AP-variant 1 strain of Anaplasma phagocytophila

Nymphal Ixodes scapularis ticks were collected from several sites in Rhode Island. DNA was extracted from a subset of these ticks, and PCR and DNA sequencing of the 16S rRNA gene were used to determine the ratio of Anaplasma phagocytophila-human agent (AP-ha) to a genetic variant not associated with human disease (AP-Variant 1). The remaining ticks were allowed to feed to repletion on either white-footed (Peromyscus leucopus) or DBA/2 (Mus musculus) mice. The engorged ticks, and blood samples drawn from each mouse at one-week intervals, were evaluated by PCR and DNA sequencing for the presence of AP-ha and Variant 1. Although a high percentage of the infecting ticks harbored AP-Variant 1, only AP-ha was amplified from the mouse blood samples. Because the A. phagocytophila variant did not establish an infection either in the natural reservoir of AP-ha, the white-footed mouse, or in a common research laboratory mouse (DBA/2), AP-Variant 1 may have an alternative natural reservoir, possibly the white-tailed deer

Inability of a Variant Strain of Anaplasma phagocytophilum to Infect Mice

Nymphal Ixodes scapularis ticks were collected from several sites in Rhode Island. Polymerase chain reaction and DNA sequencing were used to determine the presence and prevalence of Anaplasma phagocytophilum human agent (AP-ha) and a genetic variant not associated with human disease (AP-variant 1). The remaining ticks from each cohort were allowed to feed to repletion on either white-footed (Peromyscus leucopus) or DBA/2 (Mus musculus) mice. The engorged ticks and murine blood samples were evaluated for the presence of AP-ha and AP-variant 1. Although a high percentage of the infecting ticks harbored AP-variant 1, only AP-ha was amplified from the murine blood samples. Additional ticks were fed on immunocompromised SCID mice, and, again, only AP-ha was capable of establishing an infection, and only AP-ha could be detected by xenodiagnosis. These data suggest that AP-variant 1 cannot establish an infection in mice, and we propose that AP-variant 1 has an alternative natural reservoir, possibly white-tailed deer

Phylogenetic inference of Coxiella burnetii by 16S rRNA gene sequencing.

Coxiella burnetii is a human pathogen that causes the serious zoonotic disease Q fever. It is ubiquitous in the environment and due to its wide host range, long-range dispersal potential and classification as a bioterrorism agent, this microorganism is considered an HHS Select Agent. In the event of an outbreak or intentional release, laboratory strain typing methods can contribute to epidemiological investigations, law enforcement investigation and the public health response by providing critical information about the relatedness between C. burnetii isolates collected from different sources. Laboratory cultivation of C. burnetii is both time-consuming and challenging. Availability of strain collections is often limited and while several strain typing methods have been described over the years, a true gold-standard method is still elusive. Building upon epidemiological knowledge from limited, historical strain collections and typing data is essential to more accurately infer C. burnetii phylogeny. Harmonization of auspicious high-resolution laboratory typing techniques is critical to support epidemiological and law enforcement investigation. The single nucleotide polymorphism (SNP) -based genotyping approach offers simplicity, rapidity and robustness. Herein, we demonstrate SNPs identified within 16S rRNA gene sequences can differentiate C. burnetii strains. Using this method, 55 isolates were assigned to six groups based on six polymorphisms. These 16S rRNA SNP-based genotyping results were largely congruent with those obtained by analyzing restriction-endonuclease (RE)-digested DNA separated by SDS-PAGE and by the high-resolution approach based on SNPs within multispacer sequence typing (MST) loci. The SNPs identified within the 16S rRNA gene can be used as targets for the development of additional SNP-based genotyping assays for C. burnetii

Presence of Coxiella burnetii DNA in the Environment of the United States, 2006 to 2008▿

Coxiella burnetii is an obligate intracellular bacterium that causes the zoonotic disease Q fever. Because C. burnetii is highly infectious, can survive under a variety of environmental conditions, and has been weaponized in the past, it is classified as a select agent and is considered a potential bioweapon. The agent is known to be present in domestic livestock and in wild animal populations, but the background levels of C. burnetii in the environment have not been reported. To better understand the amount of C. burnetii present in the environment of the United States, more than 1,600 environmental samples were collected from six geographically diverse parts of the United States in the years 2006 to 2008. DNA was purified from these samples, and the presence of C. burnetii DNA was evaluated by quantitative PCR of the IS1111 repetitive element. Overall, 23.8% of the samples were positive for C. burnetii DNA. The prevalence in the different states ranged from 6 to 44%. C. burnetii DNA was detected in locations with livestock and also in locations with primarily human activity (post offices, stores, schools, etc.). This study demonstrates that C. burnetii is fairly common in the environment in the United States, and any analysis of C. burnetii after a suspected intentional release should be interpreted in light of these background levels. It also suggests that human exposure to C. burnetii may be more common than what is suggested by the number of reported cases of Q fever

Data from: When outgroups fail; phylogenomics of rooting the emerging pathogen, Coxiella burnetii

Rooting phylogenies is critical for understanding evolution, yet the importance, intricacies and difficulties of rooting are often overlooked. For rooting, polymorphic characters among the group of interest (ingroup) must be compared to those of a relative (outgroup) that diverged before the last common ancestor (LCA) of the ingroup. Problems arise if an outgroup does not exist, is unknown, or is so distant that few characters are shared, in which case duplicated genes originating before the LCA can be used as proxy outgroups to root diverse phylogenies. Here, we describe a genome-wide expansion of this technique that can be used to solve problems at the other end of the evolutionary scale: where ingroup individuals are all very closely related to each other, but the next closest relative is very distant. We used shared orthologous single nucleotide polymorphisms (SNPs) from 10 whole genome sequences of Coxiella burnetii, the causative agent of Q fever in humans, to create a robust, but unrooted phylogeny. To maximize the number of characters informative about the rooting, we searched entire genomes for polymorphic duplicated regions where orthologs of each paralog could be identified so that the paralogs could be used to root the tree. Recent radiations, such as those of emerging pathogens, often pose rooting challenges due to a lack of ingroup variation and large genomic differences with known outgroups. Using a phylogenomic approach, we created a robust, rooted phylogeny for C. burnetii

SupportinglnformationS2

S2. Maximum parsimony tree using seven parsimony informative (synapomorphic) SNPs with loci shared with closest outgroup species. Only one SNP locus (out of 11,386 total SNPs among C. burnetii genomes) was present in all genomes. The remaining six loci were found by relaxing the requirement that all loci are shared among all C. burnetii genomes as they were not present in the Q177 genome. All seven SNP loci were present in Pseudomonas syringae and Legionella pneumophila. Four of the seven loci were present in Ricketsiella grylli. Consistency index = 1.0. Numbers on branches indicate bootstrap support percentages from 1000 bootstrap replicates

Insertion polymorphism identified in the 16S rRNA gene of <i>C</i>. <i>burnetii</i> Mauriet.

<p>(A) DNA sequences obtained using primers E8F and E341R designate an adenine insertion at nucleotide position 213 which is confirmed in the electropherograms generated by Sequencher™ analysis software. (B) Sequence alignment shows 16S rRNA genes of <i>C</i>. <i>burnetii</i> Z3055 (GenBank accession number NZ_LK937696) and 3262 (GenBank accession number CP013667) also possess this insertion which is absent in the Nine Mile reference (Ref) strain sequence.</p