Genotypes of Coxiella burnetii in wildlife: disentangling the molecular epidemiology of a multi-host pathogen

A Novel Marine Mammal Coxiella burnetii-Genome Sequencing Identifies a New Genotype with Potential Virulence

The obligate intracellular bacterial pathogen Coxiella burnetii has been identified in a few species of marine mammals, some of which are showing population declines. It has been hypothesized that C. burnetii in marine mammals is a distinct genotype that varies significantly from the typical terrestrial genotypes. It appears to lack an IS1111. Isolates originating from Australian marine animals have a distinctly non-Australian profile of multiple-locus variable-number tandem-repeat analysis (MLVA). Extracted Coxiella DNA of Australian fur seal placental origin was sequenced using the Novaseq platform. Illumina 150 bp paired-end reads were filtered and trimmed with Trimgalore. The microbial community present in the sequenced genome was evaluated with Kraken and Bracken software using the NCBI database. A phylogenetic analysis was performed using 1131 core genes. Core genes were identified using Panaroo and inputted into Iqtree to determine the maximum-likelihood tree. A second phylogenetic tree was created using Rickettsiella grylii and using seven housekeeping genes. Results were compared with the C. burnetii Nine Mile RSA439 virulent genome. This new Australian marine mammal isolate of Coxiella (PG457) appears to be a novel genotype that lacks IS1111 and has a distinct MLVA signature (ms26, ms27, ms28, ms30, and ms31). The presence of genes for multiple virulence factors appears to give this genotype sufficient pathogenicity for it to be considered a possible causative agent of abortion in Australian fur seals as well as a potential zoonotic risk.

The Prevalence of Coxiella burnetii in Hard Ticks in Europe and Their Role in Q Fever Transmission Revisited-A Systematic Review

The zoonosis Q fever is caused by the obligate intracellular bacterium Coxiella burnetii. Besides the main transmission route via inhalation of contaminated aerosols, ticks are discussed as vectors since the first isolation of the pathogen from a Dermacentor andersonii tick. The rare detection of C. burnetii in ticks and the difficult differentiation of C. burnetii from Coxiella-like endosymbionts (CLEs) are questioning the relevance of ticks in the epidemiology of Q fever. In this review, literature databases were systematically searched for recent prevalence studies concerning C. burnetii in ticks in Europe and experimental studies evaluating the vector competence of tick species. A total of 72 prevalence studies were included and evaluated regarding DNA detection methods and collection methods, country, and tested tick species. Specimens of more than 25 different tick species were collected in 23 European countries. Overall, an average prevalence of 4.8% was determined. However, in half of the studies, no Coxiella-DNA was detected. In Southern European countries, a significantly higher prevalence was observed, possibly related to the abundance of different tick species here, namely Hyalomma spp. and Rhipicephalus spp. In comparison, a similar proportion of studies used ticks sampled by flagging and dragging or tick collection from animals, under 30% of the total tick samples derived from the latter. There was no significant difference in the various target genes used for the molecular test. In most of the studies, no distinction was made between C. burnetii and CLEs. The application of specific detection methods and the confirmation of positive results are crucial to determine the role of ticks in Q fever transmission. Only two studies were available, which assessed the vector competence of ticks for C. burnetii in the last 20 years, demonstrating the need for further research.

Investigating the Role of Micromammals in the Ecology of Coxiella burnetii in Spain

Coxiella burnetii, the causal agent of human Q fever and animal Coxiellosis, is a zoonotic infectious bacterium with a complex ecology that results from its ability to replicate in multiple (in)vertebrate host species. Spain notifies the highest number of Q fever cases to the ECDC annually and wildlife plays a relevant role in C. burnetii ecology in the country. However, the whole picture of C. burnetii hosts is incomplete, so this study seeks to better understand the role of micromammals in C. burnetii ecology in the country. Spleen samples from 816 micromammals of 10 species and 130 vaginal swabs from Microtus arvalis were analysed by qPCR to detect C. burnetii infection and shedding, respectively. The 9.7% of the spleen samples were qPCR positive. The highest infection prevalence (10.8%) was found in Microtus arvalis, in which C. burnetii DNA was also detected in 1 of the 130 vaginal swabs (0.8%) analysed. Positive samples were also found in Apodemus sylvaticus (8.7%), Crocidura russula (7.7%) and Rattus rattus (6.4%). Positive samples were genotyped by coupling PCR with reverse line blotting and a genotype II+ strain was identified for the first time in one of the positive samples from M. arvalis, whereas only partial results could be obtained for the rest of the samples. Acute Q fever was diagnosed in one of the researchers that participated in the study, and it was presumably linked to M. arvalis handling. The results of the study are consistent with previous findings suggesting that micromammals can be infected by C. burnetii. Our findings additionally suggest that micromammals may be potential sources to trace back the origin of human Q fever and animal Coxiellosis cases in Europe.

Phylogeography of Human and Animal Coxiella burnetii Strains: Genetic Fingerprinting of Q Fever in Belgium

Q fever is a zoonotic disease caused by the bacteria Coxiella burnetii. Domestic ruminants are the primary source for human infection, and the identification of likely contamination routes from the reservoir animals the critical point to implement control programs. This study shows that Q fever is detected in Belgium in abortion of cattle, goat and sheep at a different degree of apparent prevalence (1.93%, 9.19%, and 5.50%, respectively). In addition, and for the first time, it is detected in abortion of alpaca (Vicugna pacos), raising questions on the role of these animals as reservoirs. To determine the relationship between animal and human strains, Multiple Locus Variable-number Tandem Repeat Analysis (MLVA) (n=146), Single-Nucleotide Polymorphism (SNP) (n=92) and Whole Genome Sequencing (WGS) (n=4) methods were used to characterize samples/strains during 2009-2019. Three MLVA clusters (A, B, C) subdivided in 23 subclusters (A1-A12, B1-B8, C1-C3) and 3 SNP types (SNP1, SNP2, SNP6) were identified. The SNP2 type/MLVA cluster A was the most abundant and dispersed genotype over the entire territory, but it seemed not responsible for human cases, as it was only present in animal samples. The SNP1/MLVA B and SNP6/MLVA C clusters were mostly found in small ruminant and human samples, with the rare possibility of spillovers in cattle. SNP1/MLVA B cluster was present in all Belgian areas, while the SNP6/MLVA C cluster appeared more concentrated in the Western provinces. A broad analysis of European MLVA profiles confirmed the host-species distribution described for Belgian samples. In silico genotyping (WGS) further identified the spacer types and the genomic groups of C. burnetii Belgian strains: cattle and goat SNP2/MLVA A isolates belonged to ST61 and genomic group III, while the goat SNP1/MLVA B strain was classified as ST33 and genomic group II. In conclusion, Q fever is widespread in all Belgian domestic ruminants and in alpaca. We determined that the public health risk in Belgium is likely linked to specific genomic groups (SNP1/MLVA B and SNP6/MLVA C) mostly found in small ruminant strains. Considering the concordance between Belgian and European results, these considerations could be extended to other European countries.

Role of reptiles and associated arthropods in the epidemiology of rickettsioses: A one health paradigm

We assessed the presence of Rickettsia spp., Coxiella burnetii and Anaplasma phagocytophilum in reptiles, their ectoparasites and in questing ticks collected in a nature preserve park in southern Italy, as well as in a peri-urban area in another region. We also investigated the exposure to these pathogens in forestry workers, farmers and livestock breeders living or working in the nature preserve park given the report of anecdotal cases of spotted fever rickettsioses. Rickettsia spp. were molecularly detected in Podarcis muralis and Podarcis siculus lizards (i.e., 3.1%), in Ixodes ricinus (up to 87.5%) and in Neotrombicula autumnalis (up to 8.3%) collected from them as well as in I. ricinus collected from the environment (up to 28.4%). Rickettsia monacensis was the most prevalent species followed by Rickettsia helvetica. An undescribed member of the family Anaplasmataceae was detected in 2.4% and 0.8% of the reptiles and ectoparasites, respectively. Sera from human subjects (n = 50) were serologically screened and antibodies to Rickettsia spp. (n = 4; 8%), C. burnetti (n = 8; 16%) and A. phagocytophilum (n = 11; 22%) were detected. Two ticks collected from two forestry workers were positive for spotted fever group (SFG) rickettsiae. Ixodes ricinus is involved in the transmission of SFG rickettsiae (R. monacensis and R. helvetica) in southern Europe and lizards could play a role in the sylvatic cycle of R. monacensis, as amplifying hosts. Meanwhile, N. autumnalis could be involved in the enzootic cycle of some SFG rickettsiae among these animals. People living or working in the southern Italian nature preserve park investigated are exposed to SFG rickettsiae, C. burnetii and A. phagocytophilum.

Zoonotic pathogens such as Rickettsia spp., Coxiella burnetii and Anaplasma phagocytophilum are associated with ticks, lice, fleas and mites and may infect a wide range of vertebrate species. There are still many knowledge gaps concerning the arthropod vectors and amplifying hosts of these pathogens. Reptiles are known to host infected ticks with these zoonotic pathogens and eventually become infected themselves by these bacteria. Hence to address this question from a broad One-Health perspective, we assessed the molecular prevalence of Rickettsia spp., C. burnetii and A. phagocytophilum in reptiles, ticks and mites from both hosts and environment and seroprevalence in humans living or working near the same area. Rickettsia DNA was detected in lizards’ tails, Ixodes ricinus ticks and in Neotrombicula autumnalis mites collected from them and in questing ticks. Although DNA of C. burnetii and A. phagocytophilum was not detected in lizards and their ectoparasites, sera samples of human subjects tested positive for the antibodies against these zoonotic pathogens. These findings indicate the epidemiological role of lizards in spreading SFG rickettsiae as well as I. ricinus, and hence representing a potential public health concern in geographical areas where lizards, ticks and humans share the same environment.

On the possible role of ticks in the eco-epidemiology of Coxiella burnetii in a Mediterranean ecosystem

Ruminant livestock is the main reservoir of Coxiella burnetii (Cb), but little is known about the role of wildlife and ticks in its epidemiology. The Iberian ibex (Capra pyrenaica, Schinz 1838) population of "Ports de Tortosa i Beseit" (NE Spain) suffers intense tick infestations and low reproduction rates. This study aims to (1) assess the relationship between infection in ibexes (detection of serum antibodies and/or of Cb DNA in tissues) and Cb DNA presence in ticks hosted by the same ibexes; and (2) identify Cb associated risk factors. Between 2011 and 2015, serum (n = 130), spleen (n = 72), lymph node (n = 89) and tick (n = 669) samples from 134 hunter-harvested ibexes were collected. Antibody detection was performed by ELISA and Cb DNA presence was assessed by PCR. Potential risk factors were assessed with regression tree models. Although 30% of the ibexes (39/130; 95%CI, [10%-29.8%]) had antibodies, Cb DNA was detected in only 9.8% of the ibexes (11/112; 95%CI [7.6%-27.25%]). The prevalence of Cb-carrier ticks averaged 10% and exceeded 20% for the genus Haemaphysalis. However, lacking correlation between infection in ibexes and their ticks does not support tick-to-ibex transmission or vice versa. Tree modelling points to host, population and environmental factors as drivers of Cb infection in ticks and suggests connections with the domestic cycle. The percentage of Cb-carrier ticks detected is noteworthy. Along with heavy tick infestations, it suggests vector potential for these tick species, especially for the genera Rhipicephalus and Haemaphysalis. Since vector competence has not been assessed in these tick species, a classic vector role cannot be proposed nor discarded, but promoter factors of vector capacity occur. In addition, the risk of tick-borne infection through tick excreta should not be neglected. While the airborne route is the preeminent route for Cb infection, ticks' contribution to Cb epidemiology deserves further attention.

Estimating the Efficacy of a Commercial Phase I Inactivated Vaccine in Decreasing the Prevalence of Coxiella burnetii Infection and Shedding in Red Deer (Cervus elaphus)

The red deer (Cervus elaphus) is a relevant reservoir for Coxiella burnetii in Iberia. C. burnetii genotypes that infect red deer also infect humans and domestic animals. Integrated control approaches that target both domestic and wild ruminants are, therefore, required to reduce C. burnetii infection risks in Iberia, especially in wildlife–livestock–human interaction scenarios. The aim of this field experiment was to test the efficacy of an inactivated phase I vaccine [Inactivated phase I vaccine (IPIV); Coxevac^®] when used to control C. burnetii shedding prevalence and burden in red deer as a tool to prevent transmission to livestock and humans. A semi-extensively bred red deer population in which C. burnetii is endemic was used as a model of the Iberian context. Around 75% of the reproductive hinds (>1 year old; N = 441) in the population were first vaccinated early in 2012 and were then revaccinated 3 weeks later; they were subsequently revaccinated biannually until January 2014. 75% of the yearling females left as replacement in 2012 and 2013 were vaccinated in June and revaccinated thereafter following the same protocol. 25% of the population, including the replacement females, was kept as a control group throughout the study. Changes in the humoral immune response after vaccination were estimated by analyzing sera collected at 10 different times between January 2011 and January 2015. The vaccinated and control hinds were surveyed at 2.5, 3.5, and 4.5 months after calving in 2012, 2013, and 2014 to collect vaginal swabs, milk, and feces. The presence and burden of C. burnetii DNA in swabs, milk, and feces was evaluated by means of real-time PCR. Vaccination induced high antibody prevalence and levels. The proportion of animals shedding C. burnetii in vaginal secretions and milk did not change over time in the vaccination group with respect to the control group. In contrast, there was a significant reduction in the proportion of deer shedding C. burnetii in feces in both the vaccinated and control groups. The decrease in the proportion of fecal shedders coincided with a significant reduction in the incidence of infection of non-vaccinated yearling females in the population. This finding suggests that long-term vaccination with IPIV could reduce environmental contamination with C. burnetii and control transmission, perhaps making this a promising tool with which to control C. burnetii in red deer in the future.