Molecular characterization of Coxiella burnetii isolates by infrequent restriction site-PCR and MLVA typing

Molecular and genotyping techniques in diagnosis of Coxiella burnetii: An overview

Although we live in the genomic era, the accessibility of the complete genome sequence of Coxiella burnetii, the etiological agent of Q fever, has increased knowledge in the field of genomic diversity of this agent However, it is still somewhat of a "question" microorganism. The epidemiology of Q fever is intricate due to its global distribution, repository and vector variety, as well as absence of surveys defining the dynamic interaction among these factors. Moreover, C. burnetii is a microbial agent that can be utilized as a bioterror weapon. Therefore, typing techniques used to recognize the strains can also be used to trace infections back to their source which is of great significance. In this paper, the latest and current typing techniques of C. burnetii spp. are reviewed illustrating their advantages and constraints. Recently developed multi locus VNTR analysis (MLVA) and single-nucleotide polymorphism (SNP) typing methods are promising in improving diagnostic capacity and enhancing the application of genotyping techniques for molecular epidemiologic surveys of the challenging pathogen. However, most of these studies did not differentiate between C. burnetii and Coxiella-like endosymbionts making it difficult to estimate the potential role that ticks play in the epidemiology of Q fever. Therefore, it is necessary to analyze the vector competence of different tick species to transmit C. burnetii. Knowledge of the vector and reservoir competence of ticks is important for taking adequate preventive measures to limit infection risks. The significant prevalence observed for the IS1111 gene underscores its substantial presence, while other genes display comparatively lower prevalence rates. Methodological variations, particularly between commercial and non-commercial kit-based methods, result in different prevalence outcomes. Variations in sample processing procedures also lead to significant differences in prevalence rates between mechanical and non-mechanical techniques.

Using participatory epidemiology to investigate the causes of cattle abortion in Southwest Ethiopia

Cattle abortion, stemming from both infectious and non-infectious causes, lead to notable financial setbacks in the cattle industry. Between October 2020 and October 2021, an epidemiological investigation took place in Southwest Ethiopia. The objective was to determine the magnitude and seasonal occurrence of the presumed causes of cattle abortion. Information for this research was collected through 30 group discussions, each involving 8-12 participants. Various participatory epidemiological tools, including semi-structured interviews, pairwise ranking, matrix scoring, proportional piling, and seasonal calendars, were employed in the designated areas. By employing the pairwise ranking approach, the relative significance of presumed causes contributing to cattle abortion was established. The identified major presumed causes of cattle abortion, listed in increasing order of importance, were blackleg, foot-and-mouth disease, pasteurellosis, lumpy skin disease, listeriosis, trypanosomosis, Q fever, leptospirosis, and brucellosis. Participants identified brucellosis (6.1%), leptospirosis (6.0%), and Q-fever (5.7%) as the primary presumed causes of abortion, determined through proportional piling. Matrix scoring analysis indicated a robust agreement (W = 0.464-0.989; P < 0.001) among different informant groups regarding both the presumed causes of abortion and the associated clinical signs. Brucellosis and Q-fever were perceived to be more prevalent during the dry season, while leptospirosis, listeriosis, and lumpy skin disease were associated with the wet, hot, and rainy seasons. However, Pasteurellosis, blackleg, and physical/mechanical factors were deemed to be consistently encountered causes of abortion throughout the year. The patterns of seasonal occurrence of suspected abortion causes were widely acknowledged across informant groups (W = 0.977-0.863; P < 0.001). Local practices involving herbal remedies and traditional methods were employed by participants to manage cattle abortion. Moreover, the results underscore the necessity for additional laboratory research to pinpoint the exact causes of abortion in the study areas.

Genotyping and phylogenetic analysis of Coxiella burnetii in domestic ruminant and clinical samples in Iran: insights into Q fever epidemiology

Coxiella burnetii, a zoonotic pathogen, is the causative agent of Q fever, an endemic disease in Iran. However, there is currently a lack of available data on the genotypes of C. burnetii in the country. Here, we typed 26 C. burnetii isolates detected in milk, abortion, cotylodon, and cardiac valve samples from various geographical areas and hosts (7 cattle, 8 goats, 10 sheep, and 1 human) using Multilocus Variable Number Tandem Repeat Analysis (MLVA/VNTR) with five loci:ms24, ms27, ms28, ms33, and ms34. As IS1111 was observed to be spontaneously inserted in locus ms23 across all of our examined C. burnetii samples, five loci were employed for MLVA/VNTR genotyping. Among the 26 C. burnetii strains, 22 distinct genotypes (A-V) were identified in the discriminative loci. In silico analysis categorized Iranian C. burnetii strains into five genomic groups along with seven singletons, representing 11 exiting clonal complexes worldwide. Clusters 10 and 11 exclusively consisted of Iranian samples. These findings revealed high genotyping diversity among C. burnetii isolates in Iran. The genotypes circulating in Iran differed significantly from those found in other regions worldwide. To gain a comprehensive understanding of Q fever epidemiology in Iran, it is crucial to conduct large-scale studies that assess the distribution of C. burnetii genotypes across different geographical areas, hosts, and sources.

Interdisciplinary studies on Coxiella burnetii: From molecular to cellular, to host, to one health research

The Q-GAPS (Q fever GermAn interdisciplinary Program for reSearch) consortium was launched in 2017 as a German consortium of more than 20 scientists with exceptional expertise, competence, and substantial knowledge in the field of the Q fever pathogen Coxiella (C.) burnetii. C. burnetii exemplifies as a zoonotic pathogen the challenges of zoonotic disease control and prophylaxis in human, animal, and environmental settings in a One Health approach. An interdisciplinary approach to studying the pathogen is essential to address unresolved questions about the epidemiology, immunology, pathogenesis, surveillance, and control of C. burnetii. In more than five years, Q-GAPS has provided new insights into pathogenicity and interaction with host defense mechanisms. The consortium has also investigated vaccine efficacy and application in animal reservoirs and identified expanded phenotypic and genotypic characteristics of C. burnetii and their epidemiological significance. In addition, conceptual principles for controlling, surveilling, and preventing zoonotic Q fever infections were developed and prepared for specific target groups. All findings have been continuously integrated into a Web-based, interactive, freely accessible knowledge and information platform (www.q-gaps.de), which also contains Q fever guidelines to support public health institutions in controlling and preventing Q fever. In this review, we will summarize our results and show an example of how an interdisciplinary consortium provides knowledge and better tools to control a zoonotic pathogen at the national level.

Detection of Coxiella burnetii and characterisation by multiple-locus variable-number tandem repeat analysis in bovine bulk tank milk samples

Coxiella burnetii is the aetiological agent of Q fever, which is highly prevalent in Turkiye, but information on the genetic profiles of the bacterium is limited. This study aimed to investigate the presence of C. burnetii in bovine bulk tank milk (BTM) samples by polymerase chain reaction (PCR) and to investigate the genotypes by means of multiple-locus variable-number tandem repeat analysis (MLVA). A total of 25 markets that sold raw cow's milk were analysed by conventional PCR analysis. An MLVA analysis was performed at six loci, namely MS23, MS24, MS27, MS28, MS33, and MS34, to determine the genotypic variations of C. burnetii found in the positive DNA samples. The DNA of C. burnetii was detected in 16% of the BTM samples. The C. burnetii strains identified in the bovine milk samples collected in this study were found to belong to the same genotypic group as those detected in the bovine milk samples gathered in Greece. As a result, both the presence and genotyping studies of C. burnetii on the BTM samples in Turkiye will contribute to the determination of the geographical distribution of the agent.

MLVA and com1 genotyping of Coxiella burnetii in farmed ruminants in Great Britain

Coxiella burnetii, the causative agent of the zoonotic disease Q fever, has been shown to be endemic in Great Britain, but information on the prevailing genomic lineages or Genomic Groups (GGs) of Coxiella burnetii is limited. The aim of this study was to genotype C. burnetii isolates from infected farmed ruminants by Multiple Locus Variable Number Tandem Repeat Analysis (MLVA) and identify their associated Genomic Group. A total of 51 Coxiella-containing abortion samples from farmed ruminants (sheep, goats, and cattle), which were collected in Great Britain during 2013-2018, were included in the study, 34 of which returned a C. burnetii MLVA genotype. All bovine samples (n = 18), 5/7 of the ovine samples, and 3/9 of the caprine samples belonged to an MLVA cluster which we could link to the MST20 genotype of GG III, whereas 6/9 of the caprine samples and 2/7 of the ovine samples belonged to MLVA clusters which we could link to the MST33 or MST32 genotypes of GG II (7 vs 1 sample(s), respectively). We also noted that the Coxiella-specific com1 gene contained unique mutations that could genomotype isolates, i.e. assign them to a Genomic Group. In conclusion, both goats and sheep in Great Britain (from 2014 onward) were found to carry the same MLVA genotypes (MST33-like; GG II) that were linked to a human Q fever outbreak in the Netherlands. This knowledge in combination with the usage of genotyping/genomotyping methods should prove useful in future surveillance programs and in the management of outbreaks.

Genotyping of Coxiella burnetii from Cattle by Multispacer Sequence Typing and Multiple Locus Variable Number of Tandem Repeat Analysis in the Republic of Korea

Genotyping of Coxiella burnetii using multispacer sequence typing (MST) and multiple locus variable number tandem repeat analysis (MLVA) was conducted from infected animals for the first time in the Republic of Korea. C. burnetii was detected by real-time PCR, and followed by MST and MLVA genotyping. The result showed that detected C. burnetii all had the same MLVA genotype, 6-13-2-7-9-10 for markers MS23-MS24-MS27-MS28-MS33-MS34, respectively, and genotype group 61 for MST. The same genotypes were previously identified in Poland. Importantly, this MLVA type was detected in humans in France, suggesting that the Korean strain can also potentially cause Q fever in humans. MST and MLVA were very useful tools for analyzing the molecular epidemiology of C. burnetii and helpful for interpreting the epidemiological relationship between isolates from domestic and international resources.

Novel genotypes of Coxiella burnetii circulating in rats in Yunnan Province, China

BACKGROUND

Coxiella burnetii (Cb) is the causative agent of the zoonotic disease Q fever which is distributed worldwide. Molecular typing of Cb strains is essential to find out the infectious source and prevent Q fever outbreaks, but there has been a lack of typing data for Cb strains in China. The aim of this study was to investigate the genotypes of Cb strains in wild rats in Yunnan Province, China.

RESULTS

Eighty-six wild rats (Rattus flavipectus) were collected in Yunnan Province and 8 of the 86 liver samples from the wild rats were positive in Cb-specific quantitative PCR (qPCR). The Cb strains from the 8 rats were then typed into 3 genotypes using 10-spacer multispacer sequence typing (MST), and 2 of the 3 genotypes were recognized as novel ones. Moreover, the Cb strains in the wild rats were all identified as genotype 1 using 6-loci multilocus variable number of tandem repeat analysis (MLVA).

CONCLUSIONS

This is the first report of genotypic diversity of Cb strains from wild rats in China. Further studies are needed to explore the presence of more genotypes and to associate the genotypes circulating in the wildlife-livestock interaction with those causing human disease to further expand on the epidemiological aspects of the pathogen.

Serological, Molecular Prevalence and Genotyping of Coxiella burnetii in Dairy Cattle Herds in Northeastern Algeria

In Algeria, data on the epidemiology of coxiellosis in cattle are still lacking. In this study, bulk tank milk (BTM) samples from 200 randomly selected dairy cattle herds from Setif province of Algeria were analyzed by an indirect enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR). Results highlighted that 37% (95% CI: 30.31–43.69%) and 9% (95% CI: 5.03–12.96%) of BTM samples contained Coxiella burnetii antibodies and DNA, respectively. Based on Cohen’s kappa coefficient, a very low agreement between the ELISA and PCR results was found (k = 0.0849) (95% CI: 0.00–0.189). For a second experiment, 186 whole blood samples of cows from farms with reproduction disorders were analyzed by molecular tools to detect C. burnetii. This study revealed an overall prevalence of 6.98% (95% CI: 3.32–10.65%). All positive samples determined by conventional PCR were analyzed by real-time quantitative PCR (qPCR). Eleven samples with cycle threshold (Ct) values lower than 35 were selected for genotyping by the multispacer sequence typing (MST) method. The MST12 genotype in BTM samples, the MST32 genotype and a new MST genotype (partial profile) in whole blood samples were identified. Obtained results have allowed us to better understand the epidemiology of bovine coxiellosis in the region of Setif.

CoxBase: an Online Platform for Epidemiological Surveillance, Visualization, Analysis, and Typing of Coxiella burnetii Genomic Sequences

Q (query) fever is an infectious zoonotic disease caused by the Gram-negative bacterium Coxiella burnetii. Although the disease has been studied for decades, it still represents a threat due to sporadic outbreaks across farms in Europe. The absence of a central platform for Coxiella typing data management is an important epidemiological gap that is relevant in the case of an outbreak. To fill this gap, we have designed and implemented an online, open-source, web-based platform called CoxBase (https://coxbase.q-gaps.de). This platform includes a database that holds genotyping information on more than 400 Coxiella isolates alongside metadata that annotate them. We have also implemented features for in silico genotyping of completely or minimally assembled Coxiella sequences using five different typing methods, querying of existing isolates, visualization of isolate geodata via aggregation on a world map, and submission of new isolates. We tested our in silico typing method on 50 Coxiella genomes downloaded from the RefSeq database, and we successfully genotyped all genomes except for cases where the sequence quality was poor. We identified new spacer sequences using our implementation of the multispacer sequence typing (MST) in silico typing method and established adaA gene phenotypes for all 50 genomes as well as their plasmid types.

IMPORTANCE Q fever is a zoonotic disease that is a source of active epidemiological concern due to its persistent threat to public health. In this project, we have identified areas in the field of Coxiella research, especially regarding public health and genomic analysis, where there is an inadequacy of resources to monitor, organize, and analyze genomic data from C. burnetii. Subsequently, we have created an open, web-based platform that contains epidemiological information, genome typing functions comprising all the available Coxiella typing methods, and tools for isolate data discovery and visualization that could help address the above-mentioned challenges. This is the first platform to combine all disparate genotyping systems for Coxiella burnetii as well as metadata assets with tools for genomic comparison and analyses. This platform is a valuable resource for laboratory researchers as well as research epidemiologists interested in investigating the relatedness or dissimilarity among C. burnetii strains.

Molecular detection of Coxiella burnetii in small ruminants and genotyping of specimens collected from goats in Poland

Background

Coxiella burnetii is the etiological agent of Q fever, a zoonosis affecting many animal species including sheep and goats. The aims of this study were to evaluate the shedding of Coxiella burnetii in small ruminant herds and to identify the pathogen’s genotypes and sequence types (STs) using multiple-locus variable number tandem repeat analysis (MLVA) and multispacer sequence typing (MST) methods.

Results

Overall, 165 samples from 43 herds of goats and 9 flocks of sheep were collected including bulk tank milk (BTM), individual milk samples, vaginal swabs, tissue sections from stillborn kids, feces and placentas. These were tested by real-time PCR targeting the IS1111 element. C. burnetii infection was confirmed in 51.16% of the herds of goats and 22.2% of the flocks of sheep. Six out of nine samples originating from goats were successfully genotyped using the MLVA method. The presence was confirmed of two widely distributed MLVA genotypes (I and J) and genotype PL1 previously reported only in cattle. Only one sequence type (ST61) was identified; however, the majority of specimens represented partial STs and some of them may belong to ST61. Other partial STs could possibly be ST74.

Conclusion

This study confirmed the relatively common occurrence of Coxiella burnetii in small ruminant herds in Poland. Interestingly, all genotyped samples represent cattle-associated MLVA genotypes.

Multispecies Q Fever Outbreak in a Mixed Dairy Goat and Cattle Farm Based on a New Bovine-Associated Genotype of Coxiella burnetii

A Q fever outbreak on a dairy goat and cattle farm was investigated with regard to the One Health concept. Serum samples and vaginal swabs from goats with different reproductive statuses were collected. Cows, cats, and a dog were investigated with the same sample matrix. The farmer's family was examined by serum samples. Ruminant sera were analyzed with two phase-specific enzyme-linked immunoassays (ELISAs). Dominant immunoglobulin G (IgG) phase II levels reflected current infections in goats. The cows had high IgG phase I and II levels indicating ongoing infections. Feline, canine, and human sera tested positive by indirect fluorescent antibody test (IFAT). Animal vaginal swabs were analyzed by qPCR to detect C. burnetii, and almost all tested positive. A new cattle-associated C. burnetii genotype C16 was identified by the Multiple-Locus Variable-number tandem repeat Analysis (MLVA/VNTR) from ruminant samples. Additionally, a possible influence of 17ß-estradiol on C. burnetii antibody response was evaluated in goat sera. Goats in early/mid-pregnancy had significantly lower levels of phase-specific IgGs and 17ß-estradiol than goats in late pregnancy. We conclude that the cattle herd may have transmitted C. burnetii to the pregnant goat herd, resulting in a Q fever outbreak with one acute human case. The influence of placentation and maternal pregnancy hormones during pregnancy on the immune response is discussed.

Identification of Tick-Borne Pathogens and Genotyping of Coxiella burnetii in Rhipicephalus microplus in Yunnan Province, China

Rhipicephalus microplus, a vector that can transmit many pathogens to humans and domestic animals, is widely distributed in Yunnan province, China. However, few reports on the prevalence of tick-borne pathogens (TBPs) in Rh. microplus in Yunnan are available. The aim of this study was to detect TBPs in Rh. microplus in Yunnan and to analyze the phylogenetic characterization of TBPs detected in these ticks. The adult Rh. microplus (n = 516) feeding on cattle were collected. The pooled DNA samples of these ticks were evaluated using metagenomic next-generation sequencing (mNGS) and then TBPs in individual ticks were identified using genus- or group-specific nested polymerase chain reaction (PCR) combined with DNA sequencing assay. As a result, Candidatus Rickettsia jingxinensis (24.61%, 127/516), Anaplasma marginale (13.18%, 68/516), Coxiella burnetii (3.10%, 16/516), and Coxiella-like endosymbiont (CLE) (8.33%, 43/516) were detected. The dual coinfection with Ca. R. jingxinensis and A. marginale and the triple coinfection with Ca. R. jingxinensis, A. marginale, and CLE were most frequent and detected in 3.68% (19/516) and 3.10% (16/516) of these ticks, respectively. The results provide insight into the diversity of TBPs and their coinfections in Rh. microplus in Yunnan province of China, reporting for the first time that C. burnetii had been found in Rh. microplus in China. Multilocus variable number tandem repeat analysis with 6 loci (MLVA-6) discriminated the C. burnetii detected in Rh. microplus in Yunnan into MLVA genotype 1, which is closely related to previously described genotypes found primarily in tick and human samples from different regions of the globe, indicating a potential public health threat posed by C. burnetii in Rh. microplus in Yunnan.

High Prevalence and New Genotype of Coxiella burnetii in Ticks Infesting Camels in Somalia

Coxiella burnetii is the causative agent of Q fever. It can infect animals, humans, and birds, as well as ticks, and it has a worldwide geographical distribution. To better understand the epidemiology of C. burnetii in Somalia, ticks infesting camels were collected from five different regions, including Bari, Nugaal, Mudug, Sool, and Sanaag, between January and March 2018. Collected ticks were tested for C. burnetii and Coxiella-like endosymbiont DNA by using IS1111, icd, and Com1-target PCR assays. Moreover, sequencing of the 16S-rRNA was conducted. Molecular characterization and typing were done by adaA-gene analysis and plasmid-type identification. Further typing was carried out by 14-marker Multi-Locus Variable-Number Tandem Repeats (MLVA/VNTR) analysis. The investigated ticks (n = 237) were identified as Hyalomma spp. (n = 227, 95.8%), Amblyomma spp. (n = 8, 3.4%), and Ripicephalus spp. (n = 2, 0.8%), and 59.1% (140/237) of them were positive for Coxiella spp. While Sanger sequencing and plasmid-type identification revealed a C. burnetii that harbours the QpRS-plasmid, MLVA/VNTR genotyping showed a new genotype which was initially named D21. In conclusion, this is the first report of C. burnetii in ticks in Somalia. The findings denote the possibility that C. burnetii is endemic in Somalia. Further epidemiological studies investigating samples from humans, animals, and ticks within the context of "One Health" are warranted.

Proteome-wide analysis of Coxiella burnetii for conserved T-cell epitopes with presentation across multiple host species

Background

Coxiella burnetii is the Gram-negative bacterium responsible for Q fever in humans and coxiellosis in domesticated agricultural animals. Previous vaccination efforts with whole cell inactivated bacteria or surface isolated proteins confer protection but can produce a reactogenic immune responses. Thereby a protective vaccine that does not cause aberrant immune reactions is required. The critical role of T-cell immunity in control of C. burnetii has been made clear, since either CD8⁺ or CD4⁺ T cells can empower clearance. The purpose of this study was to identify C. burnetii proteins bearing epitopes that interact with major histocompatibility complexes (MHC) from multiple host species (human, mouse, and cattle).

Results

Of the annotated 1815 proteins from the Nine Mile Phase I (RSA 493) assembly, 402 proteins were removed from analysis due to a lack of inter-isolate conservation. An additional 391 proteins were eliminated from assessment to avoid potential autoimmune responses due to the presence of host homology. We analyzed the remaining 1022 proteins for their ability to produce peptides that bind MHCI or MHCII. MHCI and MHCII predicted epitopes were filtered and compared between species yielding 777 MHCI epitopes and 453 MHCII epitopes. These epitopes were further examined for presentation by both MHCI and MHCII, and for proteins that contained multiple epitopes. There were 31 epitopes that overlapped positionally between MHCI and MHCII across host species. Of these, there were 9 epitopes represented within proteins containing ≥ 5 total epitopes, where an additional 24 proteins were also epitope dense. In all, 55 proteins were found to contain high scoring T-cell epitopes. Besides the well-studied protein Com1, most identified proteins were novel when compared to previously studied vaccine candidates.

Conclusion

These data represent the first proteome-wide evaluation of C. burnetii peptide epitopes. Furthermore, the inclusion of human, mouse, and bovine data capture a range of hosts for this zoonotic pathogen plus an important model organism. This work provides new vaccine targets for future vaccination efforts and enhances opportunities for selecting multiple T-cell epitope types to include within a vaccine.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12859-021-04181-w.

Correlating Genotyping Data of Coxiella burnetii with Genomic Groups

Coxiella burnetii is a zoonotic pathogen that resides in wild and domesticated animals across the globe and causes a febrile illness, Q fever, in humans. Several distinct genetic lineages or genomic groups have been shown to exist, with evidence for different virulence potential of these lineages. Multispacer Sequence Typing (MST) and Multiple-Locus Variable number tandem repeat Analysis (MLVA) are being used to genotype strains. However, it is unclear how these typing schemes correlate with each other or with the classification into different genomic groups. Here, we created extensive databases for published MLVA and MST genotypes of C. burnetii and analysed the associated metadata, revealing associations between animal host and human disease type. We established a new classification scheme that assigns both MST and MLVA genotypes to a genomic group and which revealed additional sub-lineages in two genomic groups. Finally, we report a novel, rapid genomotyping method for assigning an isolate into a genomic group based on the Cox51 spacer sequence. We conclude that by pooling and streamlining existing datasets, associations between genotype and clinical outcome or host source were identified, which in combination with our novel genomotyping method, should enable an estimation of the disease potential of new C. burnetii isolates.

Coxiella burnetii Shedding in Milk and Molecular Typing of Strains Infecting Dairy Cows in Greece

Ruminants are considered the commonest animal reservoir for human infection of Coxiella burnetii, the Q fever causative agent. Considering the recently described importance of human Q fever in Greece, we aimed at providing the first comprehensive direct evidence of C. burnetii in dairy cows in Greece, including the genetic characterization of strains. The 462 examined dairy farms represented all geographical areas of Greece. One bulk tank milk sample was collected from every farm and tested for the presence of C. burnetii. Molecular genotyping of strains, performed directly on samples, revealed the existence of two separate clades characterized by single nucleotide polymorphism (SNP) genotypes of type 1 and type 2. The two clades were clearly distinguished in multiple locus variable-number tandem repeat analysis (MLVA) by two discriminative loci: MS30 and MS28. Whereas MLVA profiles of SNP-type 2 clade were closely related to strains described in other European cattle populations, the MLVA profile observed within the SNP type 1 clade highlighted a peculiar genetic signature for Greece, related to genotypes found in sheep and goats in Europe. The shedding of C. burnetii bearing this genotype might have yet undefined human epidemiological consequences. Surveillance of the genetic distribution of C. burnetii from different sources is needed to fully understand the epidemiology of Q fever in Greece.

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.

Q Fever: Seroprevalence, Risk Factors in Slaughter Livestock and Genotypes of Coxiella burnetii in South Africa

Q fever is a neglected zoonosis in South Africa, causing significant losses in livestock and game animals through reproductive disorders. However, there are limited studies on the extent of Coxiella burnetii infections in livestock in South Africa. Further, there is also lack of knowledge about the types of C. burnetii strains that are currently circulating in the country. Therefore, a cross-sectional, abattoir-based study was conducted to determine the seroprevalence of C. burnetii and associated risk factors, and to characterize C. burnetii strains from slaughter livestock at red meat abattoirs in Gauteng, South Africa. Of the 507 animals tested, 6.9% (95% CI: 4.9-9.5%) were positive for antibodies against C. burnetii. The seroprevalence was 9.4% (31/331) in cattle, 4.3% (3/69) in sheep, and 0.9% (1/107) in pigs. Out of the 63 tissue samples from 35 seropositive animals including material from two sheep aborted fetuses from Mangaung district (Free State province), 12.7% (8/63) tested positive by IS1111 PCR. Genotyping of the eight PCR-positive tissues from eight animals by MLVA revealed two novel genotypes, not available in Coxiella MLVA databases. It is concluded that slaughter animals pose a risk of exposing abattoir and farm workers to C. burnetii in South Africa.

Detection of Coxiella burnetii and equine herpesvirus 1, but not Leptospira spp. or Toxoplasma gondii, in cases of equine abortion in Australia - a 25 year retrospective study

Equine abortion is a cause of severe economic loss to the equine industry. Equine herpesvirus 1 is considered a primary cause of infectious abortion in horses, however other infectious agents can also cause abortion. Abortions due to zoonotic pathogens have implications for both human and animal health. We determined the prevalence of Coxiella burnetii, Leptospira spp. and Toxoplasma gondii in 600 aborted equine foetal tissues that were submitted to our diagnostic laboratories at the University of Melbourne from 1994 to 2019. Using qPCR we found that the prevalence of C. burnetii was 4%. The highest annual incidence of C. burnetii was observed between 1997-2003 and 2016-2018. The prevalence of C. burnetii in Victoria and New South Wales was 3% and 6% respectively. All the samples tested negative for Leptospira spp. and Toxoplasma gondii DNA. Equine herpesvirus 1 DNA was detected at a prevalence of 3%. This study has provided evidence for the presence of C. burnetii in equine aborted foetal tissues in Australia, but the role of C. burnetii as potential cause of abortion in Australia requires further investigation. C. burnetii is a zoonotic disease agent that causes the disease 'Q fever' in humans. We recommend that appropriate protective measures should be considered when handling material associated with equine abortions to reduce the risk of becoming infected with C. burnetii.

Development of a PCR Kit for Detection of Coxiella burnetii in Ukraine

Coxiella burnetii is an obligate intracellular pathogen and the causative agent of Q fever. In Ukraine, 28 human cases of Q fever were reported between 1997 and 2006; however, there are no state-approved, standardized molecular diagnostic assays that can be used systematically to investigate C. burnetii transmission to humans and its distribution throughout Ukraine. To address this deficiency, we followed the recommendation of the World Organization for Animal Health (OIE) and developed a confirmatory PCR for C. burnetii for veterinary diagnosis in Ukraine. The PCR assay targeted the outer membrane-associated gene com1 in C. burnetii. Oligonucleotide primers were selected that amplify a 689-bp DNA fragment of the com1 gene (primers: CoxF2 = 5'-ACYGCAGGCGTGGCGATAG-3' and CoxR4 = 5'-TGAAGGTTTTGTTGTGAGGTGGC-3'). The assay proved highly sensitive and specific to C. burnetii DNA detection (LOD = 0.37 pg/μL). Reproducibility of the test was verified by comparing the PCR results with those of a different PCR protocol and qPCR. Using the CoxF2/CoxR4 primer set and reaction conditions described here, the PCR Diagnostic Kit C. burnetii-PCR-TEST was developed and officially registered for use in Ukraine by the State Scientific Control Institute of Biotechnology and Strains (Kyiv, Ukraine) for diagnostic purposes.

New Genotypes of Coxiella burnetii Circulating in Brazil and Argentina

Coxiella burnetii, the zoonotic agent of Q fever, has a worldwide distribution. Despite the vast information about the circulating genotypes in Europe and North America, there is a lack of data regarding C. burnetii strains in South America. Here, we show the presence of novel multispacer sequence typing (MST) genotypes of C. burnetii in two clusters detected in Brazil and Argentina that seem to be distant in parenthood. Argentinian strains isolated from a tick belongs to a new phylogenetic branch of C. burnetii, and the Brazilians strains may be related to MST 20 and 61. Multilocus variable number tandem repeats analysis (MLVA) typing provided a deeper resolution that may be related to host clusters of bovines, caprine, ovine, and ticks. Our results corroborate with the reports of geotypes of C. burnetii. Thus, we highlight the need for more genotyping studies to understand the genetic diversity of C. burnetii in South America and to confirm the hypothesis of host-related genotypes. We also emphasize the importance of virulence studies for a better understanding of Q fever in the region, which may help in surveillance and disease prevention programs.

Comparative virulence of diverse Coxiella burnetii strains

Coxiella burnetii is an intracellular, gram-negative bacterium that causes the zoonosis Q fever. This disease typically presents as an acute flu-like illness with persistent, focalized infections occurring less frequently. Clinical outcomes of Q fever have been associated with distinct genomic groups of C. burnetii, suggesting that gene content is responsible for virulence potential. To investigate this hypothesis, the virulence of thirteen C. burnetii strains (representing genomic groups I-VI) was evaluated in a guinea pig infection model by intraperitoneal injection. Seven strains caused a sustained fever (at least two days ≥39.5°C) in at least half of the animals within each experimental group. At fourteen days post infection, animals were euthanized and additional endpoints were evaluated, including splenomegaly and serology. The magnitude of these endpoints roughly correlated with the onset, duration, and severity of fever. The most severe disease was caused by group I strains. Intermediate and no virulence were evidenced following infection with group II-V and group VI strains, respectively. Flow cytometric analysis of the mesenteric lymph nodes revealed decreased CD4+ T cell frequency following infection with highly virulent group I strains. These findings buttress the hypothesis that the pathogenic potential of C. burnetii strains correlates with genomic grouping. These data, combined with comparative genomics and genetic manipulation, will improve our understanding of C. burnetii virulence determinants.

Molecular typing of Coxiella burnetii from sheep in Egypt

Coxiella burnetii, the etiological agent of Q fever, is a globally distributed zoonotic disease. The disease was reported serologically in different animal species and humans in Egypt but the genetic information about circulating Coxiella strains is limited. The present study aimed to genetically characterize Coxiella positive samples, identified in abortive sheep, based on a 17-loci Multiple Locus Variable number tandem repeat analysis (MLVA) panel and Multispacer Sequence Typing (MST). Four MLVA types were found among six examined samples. While all three samples examined by MST were identified as novel sequence type (ST) closely related to human heart valve isolates from France, Saudi Arabia, USA and United Kingdom. This study provides the first genetic information about circulating Coxiella strains in Egypt and improves epidemiological data of Q fever in the country.

Current perspectives on the transmission of Q fever: Highlighting the need for a systematic molecular approach for a neglected disease in Africa

Q fever is a bacterial worldwide zoonosis (except New Zealand) caused by the Gram-negative obligate intracellular bacterium Coxiella burnetii (C. burnetii). The bacterium has a large host range including arthropods, wildlife and companion animals and is frequently identified in human and livestock populations. In humans, the disease can occur as either a clinically acute or chronic aetiology, affecting mainly the lungs and liver in the acute disease, and heart valves when chronic. In livestock, Q fever is mainly asymptomatic; however, the infection can cause abortion, and the organism is shed in large quantities, where it can infect other livestock and humans. The presence of Q fever in Africa has been known for over 60 years, however while our knowledge of the transmission routes and risk of disease have been well established in many parts of the world, there is a significant paucity of knowledge across the African continent, where it remains a neglected zoonosis. Our limited knowledge of the disease across the African sub-continent have relied largely upon observational (sero) prevalence studies with limited focus on the molecular epidemiology of the disease. This review highlights the need for systematic studies to understand the routes of C. burnetii infection, and understand the disease burden and risk factors for clinical Q fever in both humans and livestock. With such knowledge gaps filled, the African continent could stand a better chance of eradicating Q fever through formulation and implementation of effective public health interventions.

Shedding and genetic diversity of Coxiella burnetii in Polish dairy cattle

Q fever is a worldwide zoonotic disease reported in humans and many animal species including cattle. The aims of this study were to evaluate the prevalence of Coxiella (C.) burnetii shedding in Polish dairy cattle herds and to identify the pathogen's genotypes and sequence types (STs) using multiple-locus variable number tandem repeat analysis (MLVA) and multispacer sequence typing (MST) methods. The presence of C. burnetii DNA was detected using a commercial real-time PCR kit, targeting the IS1111 element. Overall, 1,439 samples from 279 herds were tested including: 897 individual milk specimens, 101 bulk tank milk samples, 409 genital tract swabs and 32 placentas. Furthermore, 30 consumer milk samples, including 10 from vending machines and 77 dairy products were also analyzed. C. burnetii shedding was confirmed in 31.54% of tested cattle herds as well as in 69.16% of consumer milk and dairy products. Among real-time PCR-positive samples, 49 specimens obtained from 49 cattle herds and 8 samples of purchased dairy products were selected for genotyping. Overall, five previously known MLVA genotypes (I, J, BG, BE, and NM) and three new ones (proposed as PL1, PL2, and PL3) were identified. Two MST sequence types were recorded: ST16 and a novel sequence (ST61). The new genotypes and sequence types need further research particularly into their pathogenicity to humans.

Role of Coxiella burnetii in the development of fever of unknown origin: А mini review

Q fever is a widespread zoonosis throughout the world in the form of numerous natural and agricul-tural outbreaks. C. burnetii infects various hosts, including humans, ruminants and pets and in rare cases, reptiles, birds, and ticks. This bacterium is excreted in urine, milk, faeces, and birth products. In humans Q fever occurs as acute or chronic disease with diverse clinical presentation, as isolated cases and epidemics. It affects various organs and systems, and in pregnant women can cause miscar-riage or premature birth. Untreated Q fever can become chronic with adverse effects on patients. Diversity in the clinical picture in the absence of specific pathological syndrome often hinders accurate diagnosis and proper etiological significance. Therefore, improvement of diagnostic methods and in particular the development and introduction of new molecular diagnostic methods is the basis of effective therapeutic and prophylactic approach. Тhe purpose of the review is to renew the interest to Q fever – on one hand, because of its serious impact on human health and agricultural systems, and on the other, the ability for development and introduction of new molecular diagnostic methods.

Genotyping of Coxiella burnetii in sheep and goat abortion samples

Background

Q fever, caused by Coxiella burnetii, is a zoonosis that presents a worldwide distribution and affects both humans and animals. The route of dispersal of the pathogen by ruminants into the environment usually involves stages of abortion and parturition, nevertheless the agent can, also, be detected in other animal samples. Therefore it is considered as important in terms of proper diagnosis, as well as, for epidemiology and surveillance purposes, to genotype the pathogen. The aim of the current study was to investigate the presence of different genotypes of the agent in animals that had suffered from abortion during a two-year survey in Greece.

Results

Sixty nine tissue samples (37 stomach contents, 11 liver samples, 21 cotyledons) were collected from 59 abortion cases in sheep (N = 45) and goats (N = 14) from 65 farms at eight different areas of Greece. Samples were screened by qPCR and positive ones were further genotyped using a 10-locus multiple loci (ms 1, 3, 7, 12, 20, 21, 22, 26, 30 and 36) variable number of tandem repeat analysis (MLVA) method.

Three genotypes were identified in sheep (A, B, C). Samples representing each of the obtained MLVA profile were further used for MST genotyping. Ten spacers (Cox 2, 5, 6, 18, 20, 22, 37, 51, 56 and 57) were amplified. A close relatedness among the identified MLVA genotypes was confirmed since they all belonged to MST group 32.

Conclusions

The current study introduces into the aspect of genotyping of C. burnetii in Greece. Further studies are needed to explore the presence of more genotypes, to associate the genotypes circulating in the animal and tick population with those causing human disease in order to further expand on the epidemiological aspects of the pathogen.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1353-y) contains supplementary material, which is available to authorized users.

Genetic diversity of Coxiella burnetii in domestic ruminants in central Italy

Background

As the epidemiology of human Q Fever generally reflects the spread of Coxiella burnetii in ruminant livestock, molecular characterization of strains is essential to prevent human outbreaks. In this study we report the genetic diversity of C. burnetii in central Italy accomplished by MST and MLVA-6 on biological samples from 20 goat, sheep and cow farms.

Results

Five MST and ten MLVA profiles emerged from the analysis establishing a part of C. burnetii strain world atlas. In particular, ST32 occurred on 12 farms (60%), prevalently in goat specimens, while ST12 (25%) was detected on 4 sheep and 1 goat samples. ST8 and a variant of this genotype were described on 2 different sheep farms, whereas ST55 was observed on a goat farm. Five complete MLVA profiles different from any other published genotypes were described in this study in addition to 15 MLVA incomplete panels. Despite this, polymorphic markers Ms23, Ms24 and Ms33 enabled the identification of samples sharing the same MST profile.

Conclusions

Integration of such data in international databases can be of further help in the attempt of building a global phylogeny and epidemiology of Q fever in animals, with a “One Health” perspective.

Coxiella burnetii isolates originating from infected cattle induce a more pronounced proinflammatory cytokine response compared to isolates from infected goats and sheep

Coxiella burnetii is the causative agent of Q fever. Although the prevalence of C. burnetii in cattle is much higher than in goats and sheep, infected cattle are rarely associated with human outbreaks. We investigated whether the immune response of humans differs after contact with C. burnetii isolates from different host origins or with different multilocus variable number of tandem repeat analysis (MLVA) genotypes. Cytokine responses were measured in human peripheral blood mononuclear cells (PBMCs) stimulated with 16 C. burnetii isolates with known MLVA genotype from goats, sheep, cattle, acute and chronic Q fever patients. Coxiella burnetii isolates originating from cattle induce significantly more IL-1β, TNF-α and IL-22 than the isolates from goats, sheep or chronic Q fever patients. Comparing the cytokine induction of the isolates based on their MVLA genotype did not reveal differences in response between the MLVA genotypes. The proinflammatory cytokine response induced in human PBMCs by C. burnetii isolates from cattle may explain the low incidence of human Q fever outbreaks caused by cattle. The cytokine profile of PBMCs stimulated with C. burnetii isolates from chronic Q fever patients resembles isolates from goats. Furthermore, cytokine responses seem to be depending on host origin than on MLVA genotype.

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.

Genome Plasticity and Polymorphisms in Critical Genes Correlate with Increased Virulence of Dutch Outbreak-Related Coxiella burnetii Strains

Coxiella burnetii is an obligate intracellular bacterium and the etiological agent of Q fever. During 2007-2010 the largest Q fever outbreak ever reported occurred in The Netherlands. It is anticipated that strains from this outbreak demonstrated an increased zoonotic potential as more than 40,000 individuals were assumed to be infected. The acquisition of novel genetic factors by these C. burnetii outbreak strains, such as virulence-related genes, has frequently been proposed and discussed, but is not proved yet. In the present study, the whole genome sequence of several Dutch strains (CbNL01 and CbNL12 genotypes), a few additionally selected strains from different geographical locations and publicly available genome sequences were used for a comparative bioinformatics approach. The study focuses on the identification of specific genetic differences in the outbreak related CbNL01 strains compared to other C. burnetii strains. In this approach we investigated the phylogenetic relationship and genomic aspects of virulence and host-specificity. Phylogenetic clustering of whole genome sequences showed a genotype-specific clustering that correlated with the clustering observed using Multiple Locus Variable-number Tandem Repeat Analysis (MLVA). Ortholog analysis on predicted genes and single nucleotide polymorphism (SNP) analysis of complete genome sequences demonstrated the presence of genotype-specific gene contents and SNP variations in C. burnetii strains. It also demonstrated that the currently used MLVA genotyping methods are highly discriminatory for the investigated outbreak strains. In the fully reconstructed genome sequence of the Dutch outbreak NL3262 strain of the CbNL01 genotype, a relatively large number of transposon-linked genes were identified as compared to the other published complete genome sequences of C. burnetii. Additionally, large numbers of SNPs in its membrane proteins and predicted virulence-associated genes were identified in all Dutch outbreak strains compared to the NM reference strain and other strains of the CbNL12 genotype. The presence of large numbers of transposable elements and mutated genes, thereof most likely resulted in high level of genome rearrangements and genotype-specific pathogenicity of outbreak strains. Thus, the epidemic potential of Dutch outbreak strains could be linked to increased genome plasticity and mutations in critical genes involved in virulence and the evasion of the host immune system.

Environmental sampling coupled with real-time PCR and genotyping to investigate the source of a Q fever outbreak in a work setting

A Q fever outbreak was declared in February 2016 in a company that manufactures hoists and chains and therefore with no apparent occupational-associated risk. Coxiella burnetii infection was diagnosed by serology in eight of the 29 workers of the company; seven of them had fever or flu-like signs and five had pneumonia, one requiring hospitalisation. A further case of C. burnetii pneumonia was diagnosed in a local resident. Real-time PCR (RTi–PCR) showed a widespread distribution of C. burnetii DNA in dust samples collected from the plant facilities, thus confirming the exposure of workers to the infection inside the factory. Epidemiological investigations identified a goat flock with high C. burnetii seroprevalence and active shedding which was owned and managed by one of the workers of the company as possible source of infection. Genotyping by multispacer sequence typing (MST) and a 10-loci single-nucleotide polymorphism (SNP) discrimination using RTi–PCR identified the same genotype (MST18 and SNP type 8, respectively) in the farm and the factory. These results confirmed the link between the goat farm and the outbreak and allowed the identification of the source of infection. The circumstances and possible vehicles for the bacteria entering the factory are discussed.

From Q Fever to Coxiella burnetii Infection: a Paradigm Change

Coxiella burnetii is the agent of Q fever, or "query fever," a zoonosis first described in Australia in 1937. Since this first description, knowledge about this pathogen and its associated infections has increased dramatically. We review here all the progress made over the last 20 years on this topic. C. burnetii is classically a strict intracellular, Gram-negative bacterium. However, a major step in the characterization of this pathogen was achieved by the establishment of its axenic culture. C. burnetii infects a wide range of animals, from arthropods to humans. The genetic determinants of virulence are now better known, thanks to the achievement of determining the genome sequences of several strains of this species and comparative genomic analyses. Q fever can be found worldwide, but the epidemiological features of this disease vary according to the geographic area considered, including situations where it is endemic or hyperendemic, and the occurrence of large epidemic outbreaks. In recent years, a major breakthrough in the understanding of the natural history of human infection with C. burnetii was the breaking of the old dichotomy between "acute" and "chronic" Q fever. The clinical presentation of C. burnetii infection depends on both the virulence of the infecting C. burnetii strain and specific risks factors in the infected patient. Moreover, no persistent infection can exist without a focus of infection. This paradigm change should allow better diagnosis and management of primary infection and long-term complications in patients with C. burnetii infection.

Molecular epidemiology of Coxiella burnetii in French livestock reveals the existence of three main genotype clusters and suggests species-specific associations as well as regional stability

Q fever is a worldwide zoonosis caused by the bacterium Coxiella burnetii. In domestic ruminants, Q fever main clinical manifestations are abortions. Although the clinical signs may differ between ruminant species, C. burnetii's genetic diversity remains understudied in enzootic areas. Here, we focused on France, where Q fever is enzootic, with the aims to (a) identify potential associations between C. burnetii genotypes and ruminant host species; (b) assess the distribution of C. burnetii genotypes both within French farms and across France's major livestock-farming regions; and (c) suggest a subset of markers for future genotypic studies. We used DNA samples collected between 2006 and 2015 from 301 females (160 cows, 76 ewes, 65 goats) aborted of Q fever within 7 different farming regions. C. burnetii diversity was determined using a multiple-locus variable-number of tandem repeat analysis (MLVA) considering 17 markers. Using a phylogenetic approach, we identified 3 main genotypic clusters divided into 12 sub-clusters. These clusters were significantly associated with ruminant species: almost all the cattle genotypes were found in a "cattle-specific" cluster whereas small ruminants genotypes essentially grouped into the two other clusters. The clusters also proved stable over space and time, some genotypes being more specifically observed in certain farming regions. We also observed some within-farm diversity but this diversity was restricted to a same genotypic cluster. Finally, we identified 6 MLVA markers that maximized the representativeness of the diversity described. Overall, we highlighted that molecular epidemiology is a relevant approach to assess C. burnetii's genetic diversity and to reveal the existence of species-specific associations and regional stability. These results will be valuable in the field to trace genotype circulation among ruminants and from ruminants to humans. Ultimately, the potential links between genotypes and virulence traits need to be investigated to adapt control measures in livestock farms.

Coxiella burnetii Genotypes in Iberian Wildlife

To investigate if Coxiella burnetii, the causative agent of Q fever, genotypes circulating in wildlife are associated with those infecting livestock and humans, multiple-locus variable number tandem-repeat analysis (MLVA-6-marker) was carried out over C. burnetii obtained from red deer (Cervus elaphus), Eurasian wild boar (Sus scrofa), European wild rabbit (Oryctolagus cuniculus), black rat (Rattus rattus), and wood mouse (Apodemus sylvaticus). MLVA typing was performed by using six variable loci in C. burnetii: Ms23, Ms24, Ms27, Ms28, Ms33, and Ms34. The C. burnetii cooperative database from MLVABank 5.0 was employed to compare genotypes found in this study with 344 isolates of diverse origin. Twenty-two genotypes from wildlife and two genotypes from domestic goats were identified. Some MLVA genotypes identified in wildlife or in farmed game clustered with genotypes of human Q fever clinical cases, supporting the idea that humans and wildlife share C. burnetii genotypes. The major part of genotypes identified in coexisting red deer and rabbits clustered according to their host of origin, suggesting host specificity for particular C. burnetii genotypes. These findings provide important insights to understand the epidemiology of C. burnetii at the wildlife-livestock-human interface.

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

Evidences point to a relevant role of wildlife in the ecology of Coxiella burnetii worldwide. The lack of information on C. burnetii genotypes in wildlife prevents tracing-back clinical animal and human Q fever cases with potential wildlife origin. To compare C. burnetii genotypes circulating in wildlife, livestock and humans, 107 samples from red deer, European wild rabbit, racoon, small mammals, goat and sheep were genotyped by polymerase chain reaction and reverse line blot hybridization. Genomic groups I, II, VI and VII were found in wildlife and groups I, II, III and IV in domestic ruminants. Livestock genotypes clustered mainly with genotypes reported previously in livestock. Genotyping confirmed previous findings that suggest that C. burnetii may display host specificity since most genotypes of sympatric deer and rabbits clustered in separate groups. Wildlife genotypes clustered with genotypes from ticks and from acute hepatitis human Q fever cases, suggesting that particular C. burnetii genotypes circulating in a wildlife-tick cycle may occasionally jump into humans through tick bites or exposure to wildlife. This finding could be behind the reported geographic variation in the clinical presentation of acute Q fever in humans in Spain: atypical pneumonia in the north and hepatitis in the south.

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.

COMPARISON OF DIAGNOSTIC EFFECTIVENESS OF METHODS OF DETECTION OF COXIELLA BURNETII IN BLOOD OF PATIENTS WITH Q FEVER BASED ON AMPLIFICATION OF 16S rRNA GENE FRAGMENTS (STANDARD PCR) AND groEL GENE (REALTIME PCR)

Aim. Comparison of diagnostic capabilities of 2 variants of PCR for detection of Coxiella burnetii persistence in dynamics of infectious process in patients with Q fever. Materials and methods. 110 samples of clinical material, obtained from patients with Q fever in an endemic region for this infection (Astrakhan region), were studied. The samples were studied in a standard PCR (marker - 16S rRNA gene fragment) and in real-time PCR (RT-PCR) (marker - groEL gene fragment). Results. Both markers were established to be perspective for detection of C. burnetii DNA in clinical material, and RT-PCR detects positive result including late stages of the disease (illness day 21 - 31). Conclusion. This study is the first Russian publication on comparison on different PCR variants for detection of C. burnetii in blood of Q fever patients in dynamics of the infectious process.

The contribution of genomics to the study of Q fever

Coxiella burnetii is the etiological agent of Q fever, a worldwide zoonosis that can result in large outbreaks. The birth of genomics and sequencing of C. burnetii strains has revolutionized many fields of study of this infection. Accurate genotyping methods and comparative genomic analysis have enabled description of the diversity of strains around the world and their link with pathogenicity. Genomics has also permitted the development of qPCR tools and axenic culture medium, facilitating the diagnosis of Q fever. Moreover, several pathophysiological mechanisms can now be predicted and therapeutic strategies can be determined thanks to in silico genome analysis. An extensive pan-genomic analysis will allow for a comprehensive view of the clonal diversity of C. burnetii and its link with virulence.

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Q fever is a zoonosis of worldwide distribution with the exception of New Zealand. It is caused by an intracellular bacterium, Coxiella burnetii. The disease often goes underdiagnosed because the main manifestation of its acute form is a general self-limiting flu-like syndrome. The Dutch epidemics renewed attention to this disease, which was less considered before. This review summarizes the description of C. burnetii (taxonomy, intracellular cycle, and genome) and Q fever disease (description, diagnosis, epidemiology, and pathogenesis). Finally, vaccination in humans and animals is also considered.

Molecular characterization by MLVA of Coxiella burnetii strains infecting dairy cows and goats of north-eastern Italy

Q fever is a worldwide zoonotic disease caused by Coxiella burnetii (C. burnetii), an obligate intracellular bacterium. In ruminants, shedding into the environment mainly occurs during parturition or abortion, but the bacterium is shed also in milk, vaginal mucus, stools and urine. In Italy few surveys have been conducted and reported seroprevalence values ranged between 10% and 60%, even if few human cases have been described. Genotyping of bacteria is crucial for enhancing diagnostic methods and for epidemiological surveillance. The objective of this study was to investigate genotypic differences of C. burnetii genotypes directly in 34 samples, collected during a 3-years survey among 11 dairy cattle and 11 goat farms in the north-eastern part of Italy using a 6-locus multiple loci variable number of tandem repeat analysis (MLVA) method. The samples analysed included 13 bulk tank milk (BTM), 6 individual milk, 11 vaginal swabs and 4 foetal spleens. MLVA-type 2 was determined as the most prevalent in cattle in this study. C. burnetii strains circulating in the studied cattle population are very similar to genotypes previously described, while genotypes from goats showed an important variability. Further investigation are needed to understand the reason of this pattern.

Validation study for using lab-on-chip technology for Coxiella burnetii multi-locus-VNTR-analysis (MLVA) typing: application for studying genotypic diversity of strains from domestic ruminants in France

Coxiella burnetii, the etiologic bacterium of Q fever zoonosis, is still difficult to control. Ruminants are often carriers and involved in human epidemics. MLVA is a promising genotyping method for molecular epidemiology. Different techniques are used to resolve the MLVA band profiles such as electrophoresis on agarose gels, capillary electrophoresis or using the microfluidic Lab-on-Chip system. In this study, system based on microfluidics electrophoresis with Lab-on-Chip technology was assessed and applied on DNA field samples to investigate the genotypic diversity of C. burnetii strains circulating in France. The Lab-on-Chip technology was first compared to agarose gel electrophoresis. Subsequently, the set-up Lab-on-Chip technology was applied on 97 samples collected from ruminants in France using the 17 markers previously described. A discordance rate of 27% was observed between Lab-on-Chip and agarose gel electrophoresis. These discrepancies were checked and resolved by sequencing. The cluster analysis revealed classification based on host species and/or geographic origin criteria. Moreover, the circulation of different genotypic strains within the same farm was also observed. In this study, MLVA with Lab-on-Chip technology was shown to be more accurate, reproducible, user friendly and safer than gel electrophoresis. It also provides an extended data set from French ruminant C. burnetii circulating strains useful for epidemiological investigations. Finally, it raises some questions regarding the standardization and harmonization of C. burnetii MLVA genotyping.

Single Nucleotide Polymorphism Genotyping and Distribution of Coxiella burnetii Strains from Field Samples in Belgium

The genotypic characterization of Coxiella burnetii provides useful information about the strains circulating at the farm, region, or country level and may be used to identify the source of infection for animals and humans. The aim of the present study was to investigate the strains of C. burnetii circulating in caprine and bovine Belgian farms using a single nucleotide polymorphism (SNP) technique. Direct genotyping was applied to different samples (bulk tank milk, individual milk, vaginal swab, fetal product, and air sample). Besides the well-known SNP genotypes, unreported ones were found in bovine and caprine samples, increasing the variability of the strains found in the two species in Belgium. Moreover, multiple genotypes were detected contemporarily in caprine farms at different years of sampling and by using different samples. Interestingly, certain SNP genotypes were detected in both bovine and caprine samples, raising the question of interspecies transmission of the pathogen.