Coxiella burnetii in domestic doe goats in the United States, 2019-2020

Coxiella burnetii is a bacterial pathogen capable of causing serious disease in humans and abortions in goats. Infected goats can shed C. burnetii through urine, feces, and parturient byproducts, which can lead to infections in humans when the bacteria are inhaled. Goats are important C. burnetii reservoirs as evidenced by goat-related outbreaks across the world. To better understand the current landscape of C. burnetii infection in the domestic goat population, 4,121 vaginal swabs from 388 operations across the United States were analyzed for the presence of C. burnetii by IS1111 PCR as part of the United States Department of Agriculture, Animal Plant Health Inspection Service, Veterinary Services' National Animal Health Monitoring System Goats 2019 Study. In total, 1.5% (61/4121) of swabs representing 10.3% (40/388) (weighted estimate of 7.8, 95% CI 4.4-13.5) of operations were positive for C. burnetii DNA. The quantity of C. burnetii on positive swabs was low with an average Ct of 37.9. Factors associated with greater odds of testing positive included suspected Q fever in the herd in the previous 3 years, the presence of wild deer or elk on the operation, and the utilization of hormones for estrus synchronization. Factors associated with reduced odds of testing positive include the presence of kittens and treatment of herds with high tannin concentrate plants, diatomaceous earth, and tetrahydropyrimidines. In vitro analysis demonstrated an inhibitory effect of the tetrahydropyrimidine, pyrantel pamoate, on the growth of C. burnetii in axenic media as low as 1 μg per mL. The final multivariable logistic regression modeling identified the presence of wild predators on the operation or adjacent property (OR = 9.0, 95% CI 1.3-61.6, p value = 0.0248) as a risk factor for C. burnetii infection.

Comparison of three Coxiella burnetii infectious routes in mice

Evidence suggests that Coxiella burnetii, which is shed in the milk, urine, feces, and birth products of infected domestic ruminants, can lead to Q fever disease following consumption of unpasteurized dairy products; however, C. burnetii is not believed to be a major gastrointestinal pathogen. Most infections are associated with inhalation of aerosols generated from the excreta of domestic ruminants. We recently demonstrated that C. burnetii delivered by oral gavage (OG) resulted in dissemination and an immune response; however, it is unclear how infection via the oral route compares to other well-established routes. Therefore, we delivered three strains of C. burnetii (representing three pertinent sequence types in the United States, such as ST16, ST20, and ST8) to immunocompetent mice in four doses via aerosol challenge (AC), intraperitoneal injection (IP), or OG. Low dose (10^5) of ST16 by OG was insufficient to cause infection, yet doses 1,000- or 100-fold lower by IP or AC, respectively, induced a robust immune response and dissemination. Despite being able to induce an immune response in a dose-dependent manner, administration of C. burnetii via OG is the least efficient route tested. Not only were the immune responses and bacterial loads diminished in mice exposed by OG relative to AC or IP, the efficiency of transmission was also inferior. High doses (10^8) were not sufficient to ensure transmission to 100% of the ST20 or ST8 cohorts. These results may provide some basis for why ingestion of C. burnetii as a mode of Q fever transmission is not often reported.

Coxiella burnetii infections in mice: Immunological responses to contemporary genotypes found in the US

Coxiella burnetii is an obligate intracellular bacterium that causes the human disease Q fever, which can manifest as an acute flu-like illness or a long-term chronic illness, such as endocarditis. Three genotypes (ST8, ST16, and ST20) of Coxiella burnetii are commonly found in the contemporary US and are associated with specific animal hosts. Although all three genotypes have been isolated from humans with Q fever, studies comparing virulence between C. burnetii sequence types have been rare. Here, groups of mice were infected via aerosol inoculation with isolates derived from cow's milk, environmental, animal, and human samples. Mice were monitored for weight loss and blood samples were takenweekly. Animals were euthanized at 2- and 12-weeks post-infection, and bacterial burden was determined for tissues by real-time PCR. The levels of anti-Coxiella antibodies and selected inflammatory cytokines were determined for serum samples. Weight loss and splenomegaly were observed in mice infected with ST20 and ST16 isolates but were absent in the mice infected with ST8 isolates. Bacterial concentrations in the tissues were lower in the ST8 isolates at 2 weeks post-infection relative to all other isolates. ST16 and ST20 isolates induced robust antibody and cytokine responses, while ST8 isolates produced significantly lower anti-C. burnetii titers early in the infection but saw increased titers in some animals several weeks post-infection. The data suggest that the ST8 isolates are less virulent in this mouse model, as they produce less robust antibody responses that are slow to develop, relative to the ST16 and ST20 isolates.

Q Fever: A troubling disease and a challenging diagnosis

Q fever is a disease caused by the bacterial pathogen Coxiella burnetii. This hardy organism can easily spread long distances in the wind, and only a few infectious aerosolized particles are necessary to cause serious illness. Presentations of Q fever disease can be wide-ranging, allowing it to masquerade as other illnesses and highlight the importance of laboratory testing for diagnosis and treatment. This review summarizes Q fever's epidemiology and clinical presentations and presents classical laboratory diagnostic assays and novel approaches to detecting this troubling disease.

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.

Ebola Virus Disease Diagnostics, Sierra Leone: Analysis of Real-time Reverse Transcription-Polymerase Chain Reaction Values for Clinical Blood and Oral Swab Specimens

During the Ebola virus outbreak of 2013-2016, the Viral Special Pathogens Branch field laboratory in Sierra Leone tested approximately 26 000 specimens between August 2014 and October 2015. Analysis of the B2M endogenous control Ct values showed its utility in monitoring specimen quality, comparing results with different specimen types, and interpretation of results. For live patients, blood is the most sensitive specimen type and oral swabs have little diagnostic utility. However, swabs are highly sensitive for diagnostic testing of corpses.

Massive dispersal of Coxiella burnetii among cattle across the United States

Q-fever is an underreported disease caused by the bacterium Coxiella burnetii, which is highly infectious and has the ability to disperse great distances. It is a completely clonal pathogen with low genetic diversity and requires whole-genome analysis to identify discriminating features among closely related isolates. C. burnetii, and in particular one genotype (ST20), is commonly found in cow's milk across the entire dairy industry of the USA. This single genotype dominance is suggestive of host-specific adaptation, rapid dispersal and persistence within cattle. We used a comparative genomic approach to identify SNPs for high-resolution and high-throughput genotyping assays to better describe the dispersal of ST20 across the USA. We genotyped 507 ST20 cow milk samples and discovered three subgenotypes, all of which were present across the entire country and over the complete time period studied. Only one of these sub-genotypes was observed in a single dairy herd. The temporal and geographic distribution of these sub-genotypes is consistent with a model of large-scale, rapid, frequent and continuous dissemination on a continental scale. The distribution of subgenotypes is not consistent with wind-based dispersal alone, and it is likely that animal husbandry and transportation practices, including pooling of milk from multiple herds, have also shaped the patterns. On the scale of an entire country, there appear to be few barriers to rapid, frequent and large-scale dissemination of the ST20 subgenotypes.

Genotyping and Axenic Growth of Coxiella burnetii Isolates Found in the United States Environment

Coxiella burnetii is a gram-negative bacterium that is the etiologic agent of the zoonotic disease Q fever. Common reservoirs of C. burnetii include sheep, goats, and cattle. These animals shed C. burnetii into the environment, and humans are infected by inhalation of aerosols. A survey of 1622 environmental samples taken across the United States in 2006-2008 found that 23.8% of the samples contained C. burnetii DNA. To identify the strains circulating in the U.S. environment, DNA from these environmental samples was genotyped using an SNP-based approach to derive sequence types (ST) that are also compatible with multispacer sequence typing methods. Three different sequence types were observed in 31 samples taken from 19 locations. ST8 was associated with goats and ST20 with dairy cattle. ST16/26 was detected in locations with exposure to various animals and also in locations with no direct animal contact. Viable isolates were obtained for all three sequence types, but only the ST20 and ST16/26 isolates grew in acidified citrate cysteine medium (ACCM)-2 axenic media. Examination of a variety of isolates with different sequence types showed that ST8 and closely related isolates did not grow in ACCM-2. These results suggest that a limited number of C. burnetii sequence types are circulating in the U.S. environment and these strains have close associations with specific reservoir species. Growth in ACCM-2 may not be suitable for isolation of many C. burnetii strains.

Coxiella burnetii Infection in a Community Operating a Large-Scale Cow and Goat Dairy, Missouri, 2013

Coxiella burnetii is a zoonotic pathogen that causes Q fever in humans and is transmitted primarily from infected goats, sheep, or cows. Q fever typically presents as an acute febrile illness; however, individuals with certain predisposing conditions, including cardiac valvulopathy, are at risk for chronic Q fever, a serious manifestation that may present as endocarditis. In response to a cluster of Q fever cases detected by public health surveillance, we evaluated C. burnetii infection in a community that operates a large-scale cow and goat dairy. A case was defined as an individual linked to the community with a C. burnetii phase II IgG titer ≥ 128. Of 135 participants, 47 (35%) cases were identified. Contact with or close proximity to cows, goats, and their excreta was associated with being a case (relative risk 2.7, 95% confidence interval 1.3-5.3). Cases were also identified among individuals without cow or goat contact and could be related to windborne spread or tracking of C. burnetii on fomites within the community. A history of injection drug use was reported by 26/130 (20%) participants; follow-up for the presence of valvulopathy and monitoring for development of chronic Q fever may be especially important among this population.

Ebola Virus Diagnostics: The US Centers for Disease Control and Prevention Laboratory in Sierra Leone, August 2014 to March 2015

In August 2014, the Viral Special Pathogens Branch of the US Centers for Disease Control and Prevention established a field laboratory in Sierra Leone in response to the ongoing Ebola virus outbreak. Through March 2015, this laboratory tested >12 000 specimens from throughout Sierra Leone. We describe the organization and procedures of the laboratory located in Bo, Sierra Leone.

Serological Evidence of Coxiella burnetii Infection in Cattle and Goats in Bangladesh

We tested 1149 ruminant sera conveniently collected from three districts of Bangladesh to identify the serological evidence of Coxiella burnetii infection in cattle and goats by enzyme-linked immunosorbent assay. We found that 0.7% (8/1149) of ruminants had detectable immunoglobulin G for C. burnetii: 0.65% (4/620) in cattle and 0.76% (4/529) in goats. A sub-set of ruminant samples was retested and confirmed by immunofluorescence assay (18/112). Although we cannot rule out false-positive reactions, our study suggests the presence of C. burnetii in cattle and goats in Bangladesh. Further studies are required to estimate disease burden at the population level and identify risk factors for Q fever in ruminants in Bangladesh.

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

Background

Coxiella 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.

Results

We 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).

Conclusions

The 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.

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. [Coxiella burnetii; paralog SNPs; pathogen evolution; phylogeny; recent radiation; root; rooting using duplicated genes.].

Molecular and Biological Characterization of a Novel Coxiella-like Agent from Carios capensis

The genus Coxiella is currently defined by a single monotypic species, Coxiella burnetii. Novel Coxiella spp. have been detected in ticks throughout the world. These bacteria have not been cultured or named, and their evolutionary relationships to C. burnetii are poorly known. A novel Coxiella-like agent was detected by PCR amplification and sequencing of DNA extracted from 64 pelican ticks, Carios capensis, from Devoux Bank, South Carolina, USA. PCR was used to amplify and characterize genes from the new bacterium. Sequences from some metabolic and housekeeping genes shared a 92-98% similarity to C. burnetii, but other genes such as the IS1111 transposon, com1, and 5S and 16S rRNA genes were not amplified by conventional PCR. Transovarial and transtadial transmission and environmental shedding of the agent were detected by PCR.

Transmission Route Efficacy and Kinetics of AnaplasmaphagocytophilumInfection in the White-Footed Mouse,Peromyscus leucopus

Anaplasma phagocytophilum was used to infect Peromyscus leucopus mice by three routes of inoculation: infected tick infestation and intraperitoneal (IP) and subcutaneous (SQ) injection of infected tissue culture cells. A set of 12 mice were infected (four tick, four IP, and four SQ), and blood was drawn at 1, 3, 6, 9, 12, 15, 21, 28, 35, and 60 days post-infection and analyzed by use of a quantitative PCR assay to assess the level of infection. An additional set of 108 mice were infected (36 tick, 36 IP, 36 SQ) and euthanized at 1, 3, 6, 9, 12, 15, 21, 28, and 35 days post-infection (four mice/time point), and blood, spleen, bone marrow, and bladder tissue samples were analyzed. Tick infection generally produced the highest average levels of infection and peaked at 9 days post-infestation in blood, spleen, and bone marrow and at 6 days after infestation in the bladder. IP injection resulted in levels of infection that peaked on day 6 (spleen) or 12 (bladder, bone marrow, and blood). A. phagocytophilum injected SQ showed low levels of infection, and the day of peak infection varied. The average level of infection in the blood drawstressed mice was consistently higher and peaked earlier than infection in the non-stressed, euthanized mice. Xenodiagnosis was used to assay a third set of 12 mice (four tick, four IP, and four SQ) on days 7 and 14 post-infection and ticks fed on tick-infected mice showed the highest rate of PCR-positive test results at both time points (day 7, 22.2%; day 14, 17.3%). These data indicate that P. leucopus mice can be infected by tick infestation, IP injection, or SQ injection but that the kinetics and level of infection are quite variable among individual mice, may be influenced by the route of inoculation, and may be further altered by common laboratory procedures such as repeated collection of blood samples.

Inability of a Variant Strain ofAnaplasma phagocytophilumto 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.

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.

Development of monoclonal-antibody-ELISA and -DIP-STICK immunoassays for Penicillium islandicum in rice grains

Monoclonal antibodies (mAbs) were raised against Penicillium islandicum, a fungus commonly isolated from stored rice grains in South-East Asia. Mice were immunized by a direct, simple method; fresh cell-free surface washings from a solid agar slant culture were injected directly into the peritoneum without prior concentration. Hybridoma supernatants were screened by ELISA. Most of the mAbs raised cross-reacted with other storage fungi and/or uninfected rice grains but there were species-specific. One of these, PI01, was used to develop ELISA and DIP-STICK assays for the detection of P. islandicum in individual grains. All inoculated grains and approximately 90% of grains in natural infected samples from Indonesia tested positively, by ELISA, for P. islandicum. This result and those obtained for discoloured grains from both Indonesia and the Philippines, 32% and 14% respectively, are higher than those obtained by direct plating of surface-sterilized grains. Heat and periodate treatment of the PI01 antigen and binding on Western blots indicate that it is a glycoprotein of Mr greater than 90,000. Hyphae of all ages stained uniformly by immunofluorescence using the PI01 antibody but mature conidia stained only weakly.